on a 98 you disable the tors by just unplugging it. You can remove the little brain under the hood if you'd like. If by "the big box on top of the" you are referring to the big thing on top of the carb, then yes, it will run fine if you keep that there...it's just kinda annoying when you are playing with the jetting to get the carb in and out. It's not necessary to remove that thing - with the tors unplugged it won't affect anything, but if you want you can get a new throttle cable and carb cap....you'll have to add an idle adjust screw as the idle adjust is currently in that big thing on the top.
did you take any pics of the cylinder before you changed the piston? if the rings were seized....it most likely needs a bore. you said that there was no play on the rod...rotate the crank to feel the bearings. If the rings seized it was probably running lean and low on oil....and if the rings were low on oil then the crank was low on oil as well. When you pull the head again and you rotate the crank, look to see if the crank has any oil on it. Normally there should be a little bit of oil pooled in the bottom of the crank. This comes back to jetting....you obvoiusly need a larger size main jet or you could spend all this money on making the motor perfect and then ruin it again in a few hours, or less!!
Do you still have the oil injection system or do you pre-mix? Stock exhaust on that one?