as above really, the interior loom inst the problem, its the bay loom. This is due to the wiring lengths in the bay being designed for the wires coming out on the opposite side.
as danny says splicing up the engine loom isnt really that hard, what you do is rip out everything that isnt to do with the ECU and engine sensors, then figure out where the pins go. Beuty of digi injection is 99% of the wiring is all self contained, with only a few wires to the fusebox. You could even have the fuel & ecu relays on rlay holders above the fusebox and keep it 100% seperate from the main fusebox, you'lkl just need a live, earth and ign live.
Alternatively you could find a 90spec MK2 for a donor and rip out the entre interior and lighting loom then swap it over. It isnt as hard as it sounds, just take it slow and you'll get it done. You need to have the carpets taken up to do it, but handily the wiring into the tailgate sepearates at the C pillar so you dont have to drag the wires out of it to 90spec the car. The lighting loom is also totally seperate from the engine loom so just plug that in as-is. Then all you need to do is check over the MK3 bay loom and dump the MK3 bits you dont want.
How far you take it is up to you! I went all the way on my mates abf, complete 90spec conversion and I used a 90spec 16v engine loom as a base, I then unwrapped the abf loom and binned everything MK3 specific and swapped in the bits from the MK2 loom, thus I ended up with a factory 90spec MK2 ABF engine loom! Took a lot of work but since I'm anally retentive about wiring I was willign to do it! (I hate splices of any kind, I wanted it to have as few cut wires as physically possible, plus I didnt want scrappy bits of wire hanging about in the bay for MK3 stuff not present on the MK2)