That would be the easiest swap hardware wise, but consider that the original poster is starting out with a Duke, so there are lots of things that will be different including the ECM which he doesn't have for a V6.
There are a couple of ways of attacking this. One is to get all of the Fiero V6-specific wiring and fuel systems from another Fiero, then use the 3.1 long block with Fiero heads (the Fiero heads are hi-perf, the 3.1 heads are not). If he doesn't have or can't get the Fiero V-6 ECM, wiring, and fuel systems, then he can swap the 3.1 ECM and fuel system in but that's basically a full-on swap, similar in difficulty and any other non-Fiero motor swap like the 3800SC.
Starting with a Duke makes it hard no matter which way he goes.