Anyone thats decided to upgrade their Shapeoko 2 to a larger, more powerful router has run into the same problem... The top Z Axis plates stick out too far and will hit your new router. I can't take credit for this idea, I found the solution here http://www.shapeoko.com/forum/ . Here are the step by step instructions. Its free, easy and it works! You will need to drill a few hole and cut off the excess material from the front of the plates.
Step 1: Other Fixes
I've seen multiple fixes on the forum but this is by far the best. My original fix was easy enough but it had a few downsides. I used spare aluminium spaces and longer bolts to move the mounting bracket away from the carriage. This cost me a small amount of valuable work space and also put more twisting force on the X Axis MakerSlide.
Step 2: Disassemble
You'll need to remove and disassemble almost everything except for the gantry itself. Remove your router, Z stepper motor, Z carriage, and finally the Z Plates. Take apart the Z plates and be careful not to loose or misplace any parts needed. I used one of the many empty plastic bags left over from the build to separate and organize my parts.
Step 3: Your Drilling Templates Are Already Made!
This mode will cut off the front mounting hole for the Z Axis stepper motor, but there is enough room at the back of the plate to make a new one. Using an M3 Nut and Bolt, flip the plates so they face in opposite directions and bolt them together tightly ensuring they are completely square. Drill through the existing holes on each plate into the opposite plate, this will make two new holes while removing the need for guesswork, measuring and maths
Step 4: Notching the Z Axis Shim Plate
Because there will be a bolt head where there wasn't before, you'll need to notch the shim plate for clearance. Mark centre of the plate between the two mounting holes, centre punch along the line and drill multiple holes to make up the notch. I used a small grinder to clean up the notch after drilling. If you have a bandsaw or grinder you could easily use that.
Step 5: Trim the Fat
Once all your drilling is done, its time to remove the excess material on the Z Axis plates that are causing the problem. To do this, you'll need to hold the Z Axis bearing and Wave Spring up to the plates to get your measurements. Hold it in place and mark where you need to cut leaving enough room so the Wave Spring won't stick out beyond the plates. Cut them down as straight as possible using a hacksaw, bandsaw, grinder, water jet... whatever you have at your disposal. I wanted my mod to looks as stock as possible so after cutting, I cleaned up the edges and sanded down the front points so they are rounded like the original.
Step 6: Paint!
Give it a quick scuff with some scotch brute pads and a shot of semi gloss black to match original.
Step 7: Shapeoko's Assemble!
Follow the original instructions to put everything back together except for 1 important part. Don't use the steel washer on the bottom side of the new hole you drilled. The Z Axis Shim Plate isn't thick enough to fit the bolt head and a washer. The washers aren't doing anything anyways.
Step 8: Lots of Room, No Compromise, One Happy Shapeoko
I was able to move my Mounting Bracket back onto the carriage and doubled nutted it to make sure it never rattles loose. You can see there is lots of clearance now.