I know the engine swap won't be to hard, but what would be the issues of the computer and stuff. the 92 has a manual and the 98 has an auto.

 

What engine and trans are you putting into the 98?

The computer is specific to year, engine, trans model and emissions. If putting a stick and 4-cylinder into the 98 previously with a V-6 and auto you will have at least the following issues:

The engine computer is for a V-6/auto and will not work with the new setup.

The 92 engine has a recirculating fuel system, the 98 does not.

The 92 has a distributor, the V6 no.

The 98 may use A/F sensors not 02 sensors as on the 92.

The 98 has an auto shifter built into the console. The manual a stick shift setup. The trim parts from the 92 are not going to fit the 98. You will need to add a clutch pedal, the 92 may not fit.

If you change the computer the 98 wire plugs may not fit up and even if they do you will need to do a lot of rewiring.

 

I was hoping to put the 4cyl in place of the V6. leaving the Auto Trans in.

 

one certain way to do this conversion and have no issues
gather up stuff for a 4 cyl 98 and transfer all the engine bay wiring loom
its computers motor and gear box

not sure if you will require the 4 cyls driveshafts, hubs , brakes out to the wheels