Hey, I split your question off to make sure you get the answers you need. Just start a new topic next time.
Anyway, yes you will run into some problems with wiring of your new H22. First off, get an ECU to match your engine. Howver, you're going to want to get a 96 computer, since the 97+ came with an immobilizer on the ECU.
Your best bet is to buy a conversion harness for the engine, or just get a whole new wiring harness from a 96+ Lude. You could also wire it manually, if you have the knowledge and a Helm's, but that would take the longest and probably give you the most headaches.