Kain,
Have you tried testing & seeing if you have or are getting fuel from pump?
An easy way to confirm, you can loop a wire from the FB to the B+ (same place when you loop to get fault codes) & then switch on ignition, as soon as switch on key to ign, you will hear the FB activate, (buzzing sound), if that works, proceed & crank it over & see how it runs.
Once it is running you should be able to disconnect the loop wire... then see what happens ;-) 

My mechanic did with a dodgy test - he cracked the banjo bolt on top of the fuel filter, and when cranking there was enough pressure to have a decent jet of fuel spray out.
 
I like your method much better, to be honest :P

That test only confirms operation of fuel pump... not whether it is creating enough pressure, or if the FPR is doing its job. Not really a fan of that test! Surely he had an adapter that would have allowed him to plumb a gauge to read the line pressure.
 
You can't always see the capacitors failing on an ecu. Unless you try a known working one of the same part# you haven't 100% eliminated it as a possible failure mode.
 
has ignition timing been checked?

 
One thing I found that causes strange idling problems after a 3sge motor swap.
If any of the small hoses from the end of the intake manifold to the ACIS, as well as the routing down on the side of the intake manifold that goes to the fuel regulator valve have been removed and not put back correctly. 
The 2 vacuum valves there should also be tested for correct operation.
 
You would need the service manual diagram to check that out.
This one-> http://www.mr2australia.com/mr2play/tm.aspx?m=87772
Look on page EG 266 and EG 269
Even though the manual is for the gen3 motor it also applies to the gen2.
 

Thanks guys, I appreciate all the suggestions and input!
 
You're right James, but at that point the only question was 'do we have air, fuel & spark', in the initial stages of diagnosis. Fair point on the ECU as well, I haven't crossed it off the list but there are more likely suspects to pursue first - that MAP sensor code is the next on my hit list. By ignition timing I assume you mean static timing/adjustment of the dizzy - yeah that's been checked.
 
Reddtarga - None of those vac lines were removed, but I will check them out. I don't have much experience in telling the difference between the two, but my issue doesn't seem like a vac-leak though, more like ignition breakup/problems. Thanks for the engine manual too, I've got the gen2 version but more reference material is always good :D

Okay, I was able to work on the car over the weekend, still no luck though. Here's what I've found:

• Tried a known-good coil & ignitor (courtesy of Eric), no change.
• Checked through the vac lines, no leaks or missing hoses found
• Car revs easier and is less likely to want to bog down when MAP sensor is removed

I'm still searching for a MAP sensor to buy or borrow, let me know if you have one for an NA!

I would be checking all your hoses had similar prob with 3sgte changed out everything to eventually find a cracked vaccum line

I had similar issues, turned out to be the MAP sensor, i've gone through two of them now! as Rob suggested ^ vacuum leaks from hoses are worth checking over.

Thanks everyone for your suggestions, I've finally found & solved the problem. Just in case someone stumbles over this in future, the issue was a faulty distributor, and the key symptom was a check engine light on beneath 2500 RPM, and off over 2500 RPM, but no logged code. All resistance tests of the distributor checked out as per the BGB, but swapping the part made the issue go away.