VW Beetle Golf Jetta Automatic to 5 Speed Swap

Note this is for the TDI only, the 1.8T and VR6 are similar, but wiring, and programming are almost 100% different.

So... why do you want to swap?
1) the 01m automatic transmission is junk... and at $4500 used, it's expensive junk
2) the 02j 5 speed is not junk, and at $600-$1000 used, you can save a lot of money converting.
3) The automatic TDI only gets about 35 MPG real world, where the manual is capable of delivering a prius challenging 50 MPG.
4) It's the "green" thing to do...
5) Your automatic transmission just died... and you want to save some money, and get better economy to boot.

This is my first instructable, Thanks to everyone who voted for me in the Epilog Challenge! I don't think I'm going to win, but hey it's not a bad try!

Who is this for?
This instructable is for owners of any Mk4 VW Golf/Jetta/Beetle... a.k.a. 1998-2006 beetle, 1999.5-2005 jetta, and 1999.5-2005 Golf. This one is specifically from a 2001 Beetle TDI ith occasional shots from a 2003 Jetta TDI. It's for the budget conscious, or for the green, or for those who want a little more power.

Notable DIfferences
The automatic has a different:
Coolant pipe
Power steering line
Injection Pump
Axles
Transmission Computer (the manual doesn't have any wires, other than the speed sensor and the reverse switch)
Transmission (Duh!)
Shift Linkage (Duh!)
Clutch Pedal... not there (Duh!)
Starter
Wiring Harness (Duh!)
Park Neutral Relay

Since there are all of these differences, we're not going to use the transmission, transmission computer, axles, Starter, chunks of the wiring harness, park neutral relay, and probably a bunch of other stuff that was left out just because we're a bit lazy, or didn't take that photo... We're going to adapt the existing harness for clutch cancel, cruise, and reverse switch later on... we're also going to adapt one of the brackets from the automatic wiring harness to support the power steering line.

What we need
Electrical:
"53" relay (horn relay)
Red 3M crimp butt connectors
Reverse switch (should come with the transmission)
Clutch Switches (there are two on the clutch pedal, make sure you get the two brackets)
Mechanical:
Shift Linkage, complete with shift boot and shift knob, there are two boot types, so it might take two tries before you've got it right
Clutch Pedal
Transmission from a TDI (if yours is a 2.0 or 1.8T, try to get one from a TDI, it's got better gear ratios)
Manual Transmission Starter (the automatic one won't work)
Manual Transmission Axles
Dust Tins from the Engine (it's between the transmission and engine, and comes with two pieces)
All of the nuts and bolts that were removed from the junkyard
New Stuff Needed:
1x New Clutch (might as well throw in a G60/VR6 from www.dieselgeek.com or www.dieselgeek.com )
1x Dieselgeek.com sigma5 short shifter (the OEM shifter won't clear the power steering line).
2x Nuts for the wheel end of the Axles, these are one time use only!
12x Bolts for the manual transmission end of the axles, these are also one time use only
1x bottle of blue threadlocker
2x Vertical bolts for the transmission mount (again, stretch bolts!)
2L VW Gear Lube for the 02j transmission
Tools:
Yes, you will need a LOT of tools for this job
Special Tools:
VAG-COM from www.ross-tech.com
M8, M10, M12 Triple Square bits
Clutch Alignment Tool (might come in the clutch kit)
Transmission Jack (will make it MUCH easier than bench pressing the puppy in and out!)
Continuity meter (normal VOM will work)
30mm 12 point socket

Good Luck, and try to keep up!

Step 1: Prepare for the Swap! Remove (almost) EVERYTHING!

First things first, don't try this unless you've got a flat area, jack stands, wheel chocks, and some help!

Preperation:
Loosen the front lug nuts (they're acutally bolts, so remember DON'T REMOVE THE BOLTS!!!)
Jack the car up, support it, and chock the wheels
remove both front tires

Have someone step on the brakes while you complete the following:
Remove the 30mm 12 point nuts holding on the axles to the wheel hubs.
Remove the M10 or M12 bolts holding the axles to the transmission

Start removing the axles:
Remove the 16mm bolt from the front of the A arm to the sway bar, and move it out of the way
Use a Three arm puller (or axle shaft removal tool) to push the axle out of the hub, then turn the wheel one way or the other to remove both axles.

Remove the transmission:
Go under the car, on the back of the automatic transmission dust tin is a plastic cover, remove the cover
Rotate the engine to remove the three 15mm nuts from the torque converter
Remove the battery, tray, and air box
Remove all wiring harnesses from the automatic transmission
Remove the Power Steering line from the automatic transmission mount
Remove the shift linkage using a pry bar
Unplug the Transmission cooler hoses and use a 5/8" coolant hose coupler.
Remove the Starter
Remove both upper bolts from the top of the transmission
Support the engine with an engine support
Remove the two Transmission mount bolts (18mm bolts)
Remove the lower transmission mount, this can be a pain, but it will help facilitate the removal of the transmission greatly.
Rotate the engine and transmission slightly forward using a screwjack between the engine and the subframe (the car comes with one in the trunk.. A.K.A "The Widowmaker Jack")
Place transmission Jack under transmission
Remove the four lower transmission bolts
Remove transmission (yeah, I make it sound easy!)

Prep the block!
Remove the flexplate and the dust tins on the engine... an impact would be nice here, or have someone counterhold the engine on the other side... this should be a 17 or 18mm 12 point socket.

Remove the Shift linkage:
Remove three bolts holding the downpipe to the turbo
Remove two 13mm bolts holding it to a cross member
Loosen two 17mm nuts holding a pipe clamp in place.
Slide pipe clamp to the rear of the car (sometimes this requires a hammer)
Remove the downpipe from the car
Remove the Front Heat Sheild from the bottom of the car to expose the Shifter assembly.
Remove the two bolts from the shifter assembly
Go back into the inside of the car
Beetle:
Remove the console, see your manual it's a bit complicated... We've got most of it in photos below... but your mileage may vary!
Golf/Jetta:
Remove ash tray
Remove cigarette lighter assembly
Remove Metal cross brace
Remove the Shifter handle by putting the car into neutral, then pull the thumb lever out, then yank the whole thing off HARD.
Remove the metal cover
Remove the plastic PRND321 cover by snapping it off
Remove the shifter trim slider by snapping it off
Remove the two wiring harnesses
Remove the Shift Lock Solenoid wire
Remove the two 13mm nuts, and the shifter should drop out

Now for the rest of the removal story...

Step 2: Remove and Rewire!

So you thought the previous was easy... well... most people can get that far in a day, so now that you've burned off the first two hours of your day... here's more!

Disassemble the knee plates (Beetle version, Golf/Jetta is similar)
Remove the fuse panel cover
Remove the Headlight switch by pushing in and turning the switch, then pulling the switch out
Remove the dimmer switch
Remove the cover plates on the hazard switch panel
Remove the four screws on the Hazard switch panel
Remove the six screws on the knee panel
Remove the knee panel
Remove the four screws on the Metal knee panel
Remove the metal knee panel exposing the relay panel
Remove the two 10mm nuts holding on the relay panel
Remove the 175 relay (we're going to be using the socket for the 53 relay shortly)
Remove the insulation covering the firewall where the clutch pedal will go
Remove the plug where the clutch goes

Please reference your Bentley manual for actual pin-outs, and wire colors as these vary by year/model, also make sure to check for continuity on all items.

Connect Reverse lights
Cut the transmission range connector off of the wiring harness this is the connector on the back of the transmission near the ABS pump.
Use the Black/Green wire to one side of the reverse switch 
Continuity check the Yellow/Blue or Grey/Red wire from the 175 relay socket to the matching color on the Transmission range switch wiring.
Cut this wire at the 175 socket
Cut the Black/Blue wire with enough wire to spare a butt connection later for the clutch cancel switch and connect side that leads into the harness to the yellow/blue or the grey/red wire in the previous steps. This is a standard butt connection that connects the reverse switch to the reverse lights. Heat shrink this connection
Connect the transmission range side of the Yellow/Blue or Grey/Red to the other side of the reverse switch. Heat shrink these connections

Connect Clutch Cancel Switch
Cut the brown wire at the 175 relay and connect it to the Grey or White clutch pedal switch (on the top bracket)
Connect the other wire from the switch to the Black/Blue wire you cut for the reverse lights in the above underlined and bold step.

Connect Cruise
Cut the Green/Black wire from the backside of the 175 socket (should be pin 5, or the one directly in the middle of the socket) and connect it to the blue or black clutch pedal switch (the bottom one)
Cut the Grey/Red (yellow/green on 2000+ vehicles, should be Pin 9)
Check for continuity on the Grey/Red or Yellow/Green wires in the TCU connector to the grey/red or yellow/green on the 175 socket
Connect the Grey/Red or Yellow/Green wire on the 175 socket to the other side of the blue or black clutch pedal switch
Remove the TCU from the car
Pull apart the TCU connector
Disconnect the ECU harness and pull apart the large connector
There will be a yellow/red wire that has continuity with pin 19 in the ECU large connector. Cut this wire at the TCU
Connect the Yellow/Red wire in the TCU to the Grey/Red or Yellow/Green wire in the TCU.
Move the wire from ECU pin 19 to pin 66 (98 and 99 beetles are pin 44 so verify the connector pin in your bentley before doing this).
Heat shrink the Butt connectors.
Wrap the unused connectors in Gaffers tape or other harness tape. (You may also cut the unused harness out of the loom).
Reassemble the relay panel
Place a 53 relay into the modified socket.

You now can start the car! (almost!).

Step 3: Start Instaling Stuff

Just when you thought we were done removing stuff... we are!

Basically everything after this point is annoying little stuff, so we're in warp gear.... break out the service manuals for torque information! There won't be as many photos, since there isn't much to show... no secrets, just a little cursing when you can't get the transmission in on the first stab...

What Next?
Now time to stab that shifter, put the heatsheild back in place, and put the exhaust back! (yes that's one of the steps... do it now!)
Stab the clutch pedal without the hydraulic line installed... three 13mm nuts hold it to the firewall
Mount the clutch pedal bracket that braces it with the brake pedal, put the clutch switch bracket on this stud.
Mount the sensors on the clutch pedal as stated in the wiring on the previous page, the cruise goes on the bottom, the cancel goes on the top bracket
Put the hard hydraulic line on the clutch pedal under the hood
Put the soft clutch line on the clutch pedal under the hood
Cut the Brake fluid reservoir nipple where the soft clutch line connects
Quickly put the soft clutch line on the reservoir.

Install the Clutch
Don't forget to align the clutch before and during tightening the pressure plate

Install the transmission
Don't forget to lube the input shaft
Install the starter
Install the dieselgeek Short Shifter, and adjust
Install and Bleed the Slave Cylinder, verify clutch pedal has feel to it
Dont forget the transmission mount below!
Plug in the reverse light switch

Install the Axles
Install the axle heat sheild

Install the Swaybar

Install the airbox, battery tray, battery, etc

Now on to the key on test!

Step 4: Sir Not Appearing in This Film

Now for the key on test...

First key on means you don't start the car... it's just keying on to check lights, program the computer, etc.

Key on
Now, open your VCDS software with the cable plugged into the DLC connector under the drivers side dash you should still have apart
Go to Engine
Go to Coding
Change the coding from 1 to 2
Save
Exit
Key Off
Key On
Go to Engine
Go to Fault Codes
Clear Codes
Exit
Exit

Now your car is configured for a manual transmission car.

put the car into reverse, you should have reverse lights, remove the car from reverse

start the car briefly, check for unusual noises

mount the tires, and take it for a quick spin
check cruise control and that all gears work properly

Come back and reassemble the interior in the reverse order you took it apart and you are DONE!

Now you too can have 50 MPG at 65 MPH!