Engine keeps cutting out during idle. Continuous engine check light. Beams

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)

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?

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.

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

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.

Update:

• Checked PCV - ok
• Checked all fuses
• Unplugged Idle control valve sensor - still does the same thing, but at even lower idle. So ICVS working.
• Tried reading codes but no errors came up
• Noticed the throttle position sensor was wrong part number compared to Beams spec. Will look at this next.

My original body harness (with Gen 2 3SGE) was spliced with the Beams engine loom. 
But failure to read codes at all is still pointing towards loose ECU connection I suppose. 
 
I was about the clean the ICVS but there's quite a bit of plugs and hoses attached to it, plus the coolant hoses are connected so I pussied out lol. TB was clean when I opened up but I will sum up some courage to try tomorrow anyways while it's easily accessible. 

No wiring guys work at IDB....
 
Who did the wiring for you?