92 5sfe has gone south, I have a 91 3sfe available are there any issues in swapping from the 5sfe to a 3sfe?

Completely swap the engine management out, higher emessions, worse performance, much weaker parts.

a 91's 3sfe engine will work fine in your setup- just remember what Toysrme said, your emissions will be alot different and the parts on a 91 are alot crappier

a 91's 3sfe engine will work fine in your setup- just remember what Toysrme said, your emissions will be alot different and the parts on a 91 are alot crappier

Using the 3sfe is a matter of $ and ease as I already have it. Could I jsut trade over the intake setup from the 5sfe to the 3sfe and thus avoid having to trade the engine management unit?

No. You need to get a 5s-fe. It's a very common engine, you should have no problems finding one used, or plucking one from a junkyard for $100-150.

Scrap your 3s-fe. You're going to spend more money in electronics to run it than you are buying another 5s-fe.