If I got a B&M megashifter for my 88 IROC would it be alright on my transmission? My trans has 177,000 miles on it but i have a new motor with about 13,000 on it. Would it be rougher then a regular shifter is or should i be ok if i got one?

It will be fine. The shifter is not going to do anything to your transmission. The only difference between it and the stock one is you can ratchet through gears without worrying about overshifting. Don't sweat it and have fun installing it.