Will any 3.1 long block work or do you need a special year? Thanks

Any 3.1L "long" block will work. If you want to use the Fiero heads (bigger valve's than most 3.1L) you need to change pistons. 3.1's have aluminum heads, Fiero's have iron.
You do need parts from an 1988 2.8L for fiero's. (Flywheel, harmonic balancer) Because the 3.1's and the 88 2.8's are internally balanced where the 85-87 2.8's are externally balanced.

What would you change the pistons too?

Check my post in the OFF Topic Section...