Problems with V6 swapped MR2

In reply to Nockenwelle :

I am assuming the 12V source is the heater element and the 5 v is a sensor reference. So the 12v bus is still good with the sensor plugged in.

In reply to ГУЛАГ мальчик УР следующий :

The car was running, we had a fuel line leak, so I replaced all the fuel lines since they were challenge budget items. Car ran fine, took it out for a 30 min drive, and had a clunking with shifting.

Put the car us and fount the right motor mount not tight, and the left side trans mount was not installed properly. We fixed both items and went to take car out for another test drive and that is where we are. We have looked at the wiring many times by may people in both areas and cant find a problem. 

Ok guys, first I want to thank everyone for their help and suggestions, then provide you with the close to final solution. It was suggested earlier that the MAF could be installed backwards, it only fits in the housing one way and we tried flipping the housing but had the same result so we flipped it back. Last week we pulled the upper intake and found some issues with the egr plumbing and we thought a vacuum leak but were still having the same issues.

So yesterday we swapped the MAF again as a test and the car runs. I knew is was something simple, just didn't catch it with everything else, Although I still have a vacuum leak. Does anyone know what this system does? There is vacuum at this port and when I block the hose it sounds like it creates another vacuum leak under the upper manifold, but I cant see what might be causing this.

This is not shown in the standard vacuum diagram, and I cant seem to find it  in any of the books I have.  Yes I know there is another hose missing, it has been removed to get re routed and replaced. This is the standard Vac Diagram and the hose is the upper picture is not shown.