I-Speed can reflash '99-'01 RS ECUs, and there is opensource for '05+ 2.5 liter ECUs, but other than that you really have no options except piggybacks. Rallitek is supporting the PP6 pretty well, and they should be willing to help you out quite a bit to try to tune the 1.8. I wouldn't bother with much else as a piggyback at this point though.
The FWD gearboxes are different than AWD, and I don't think the OBX diff will work, but I could be wrong there. It's not a clutch type so it will be happy with whatever gear oil you are using if it does happen to fit.
I would go with what Scotty said and just grab every running 1.8 engine you can come up with, fix the external leaks if any, and consider them wear items. Other than a full exhaust and a hybrid intake, there's nothing you can do that would make a real difference.
The brake plan sounds good to me. Porterfield (or their AKAs) will make any compound in any standard brake pad/shoe configuration for a decent price. also make sure your rotors aren't wearing down. They're super cheap (like $18 each at NAPA cheap) so I'd grab a pile of those and every time they lose a few mm in cross section, scrap them for new ones instead of turning them.
The limp-mode issue sounds like a bad sensor, probably MAF but could be IAC and/or TPS or something like that. Try just swapping over the spare motor as soon as you can patch the oil leaks and see if it goes away.
I have an old OBDI fuel tank I'll sell you cheap if you want it. Dent free and the pump works fine. Also it will enable your future AWD swap should you decide to do that.
Oh, the trunk release- look at the latch on the trunk, there should be a little lever sticking out. Make sure it's down.
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FWD is the new AWD
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