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You can use the opto-isolated relay boards like these and save yourself a lot of work and make it smaller too by eliminating all of the extra parts and connect a IO pin directly to the relay board. I have a few 8 channel controllers using an Pro-Mini with a HC06 bluetooth for the interface and the 8 channel versions of this single channel board. http://www.ebay.com/itm/like/151526058542?lpid=82&...
It sounds like your controller might be setup for fractional stepping - something about 16/th step per pulse and not 1 step per pulse.. Most controllers have a programmable micro-stepping ability either in software of via switches.. My controllers (TB6600) use switches to set the micro-stepping for smoother and more precise control of the motors. I use 1/6th steps on 400 step motors requiring a total of 6400 pulses per rev.
Bad idea.. Cooling the exhaust temps by any amount is a very bad.. as a former firefighter I can tell you for certain it is an unsafe thing to do which is why the stove maker does not do it either.. Chimney fires are very real issues with things like this..If you want to recover heat do so at the firebox.. not the chimney.
Sweet job there... Here is some help on the speaker box and port design... It is a box/port calculator.. It will change the entire game when it comes to the sound as you will get the proper dimensional information for the speakers in use.. remember that generally you just multiply the resultant information by the number of speakers in use.. Good luck on the next project..
Also on a side not.. Put the batteries in series/parallel .. (2 sets of 4 in series then put those 2 sets in parallel ) and drop the dc-dc converter.. just add in an adjustable LiPo charger and adjust it to 14.8 V (or scrounge one from an old drill charger). Much, much better battery performance offering FULL current needed for the amp.. And possibly even better might be to use a 14V utility tool battery pack and charger.. such as the types used in B&D, Ryobi or Dewalt drills.. Cheap drills from Harbor Freight work great for these type of projects as they are inexpensive.. 2 of them makes for a very quick change/charge unit.. You can scavenge the connector from one of the charger bases and put that into the box to accept the battery and use the 2nd to charge them with..