Hi, if you change the battery wires to larger gauge it will not do any good unless you change all wires in cart.
After you cut the lead terminals off, strip back the insulation 1/2" and examine the copper strands for corrosion, if none is evident then go ahead and use it. Most only need to be 6" long, so I know what you mean about them being too long.
Essentially keep cutting the cable back till no corrosion, or just get some new 2 gauge welding cable and make new.
If you do not mind, can you fill me in a little on the programming of that controller? Such as did you have to buy a hand scanner, patch cord? Any info you can give I would appreciate it.
I have worked on a bunch of Bad Boy's but not on the new controller.