That time has come again for me to request the help of this good community. Sorry if it's a long one...
Anyways I've had an engine swap from 2nd Gen 3SGE to a Greytop Beams and it has been wired up by a reputable auto elec. Fuel lines and coolant piping have been routed and secured properly by reputable mechanic. There are no vacuum leaks. Fuel filter was done last year. 
Here's the problem
http://www.youtube.com/watch?v=KK6W322xhtE&feature=youtu.be
As you can see in the video the engine keeps cutting out at just above 1k rpm, right after the engine light comes on. Cycle continues. That video was taken after I changed spark plugs and added more 98 with a bit of fuel injection cleaner
Initially the mechanic thought it was maybe wiring issue or AFM so auto elec came down to test AFM. Problem is still there. What makes this really hard is that TWO diagnostic tools cannot communicate with the ECU. Auto elec then tried forcing fault codes intentionally to see if the ECU was doing it's job at all. Still no change. We then deduced it was maybe a faulty ECU.
Auto elec came around with a borrowed Beams ECU and like music to my ears, the engine idled smoothly. I then went and bought one for myself. Plugged it in and the problem came back!! What are the odds of having 2 faulty ECUs?? Luckily there was a fellow Beams owner that was local and had 2 spare Beams ECUs. Tried both but to no avail. I then wanted to see if my original Beams ECU was actually faulty or not so I tried it on his car. To my surprise, his car ran fine!!
 
I'm not sure what to look for next. I'll attempt a compression test on the weekend but I hear you need a warm engine to get accurate readings. With the car running like **** (extremely rich) I'm not sure how I could get it warm without damaging the internals (from thinning of oil?).
Worst case I guess I might have to take it to IDB (but I'm kinda broke right now T_T)

It just doesn't make any sense that the borrowed ECU worked and 3 others didn't but the others worked fine on the other car...

So no fault codes were displayed when you put it into diagnostic mode? (Check engine light flashes)
Was the part number on the ecu that worked the same as all the rest?

Id take it back to IAN as he has knowledge about these engines afaik, and is probably a safer bet than letting someone with no prior knowledge of the engine tinkerign with it. (not having a go at anyone )
 
just out of curiosity u mentioned an AFM, i was under the impression the beams didnt have one.
also are these obd2 engines, if so didnt a scanner pick up anythign at all?
 
also as skylighter mentioned, was the ecu part numbers the same, see if you can buy the ecu or swap it for your one off the mechanic even.
 
lets hope its a simple solution and ur up and running soon
cheers

Well according to auto elec, when it's a continuous non stop flash it means engine has no faults I think, meaning ECU is telling us everything's okay so he said it was a bit weird engine was hunting. When he tried pulling out some plugs (idle control i think) it still wouldn't give us any fault codes.
That ECU in the video was from a Redtop Beams Celica, I tested with another Celica ECU and another Greytop ECU. They are all interchangeable.

Auto elec said it runs AFM not MAF. If the wiring or ECU is faulty, the scanner will have trouble reading apparently. I think for me the simplest solution is to swap my ECU with the one that auto elec borrowed off his mate's and somehow magically worked. I mean if my one works on his then he's got nothing to lose? 

Did you drive the car when it had the ecu that worked in it?
Has the AFM been tampered with?

yeah constant flashing means everything is ok.
could there be a possible revision change between the ecu,s like the gen 2 turbos have and maybe thats what is causing the issue. just a thought.
ideally i would try and swap the ecu for the running one and see if the car drives properly along the rev range and test your one on the other car and see if it works well.

Swapped another AFM to see if mine was faulty but still did the same thing so shouldn't be the AFM. I got to drive it around the block once with the working ECU. Short lived happiness.

loose wire on the timing sensor :) (i dont know about beams but the older engines will idle without a timing input to the ECU then missfire and die when you try and build revs.)
 
probably loose on the plug that goes into the ECU and when you plug out/in its just luck if the wires in the right spot. a bit like when your headphones start cutting in and out and you have to get the cord just right till you decide its all too much and get new ones...
 
thats my GUESS. 
 
check the wiring in the ECU plug and make sure its solid... hopefully its not a break in the wiring.
 
out of interest is it a new loom or your original one?