V6 replaced into car that was a Supercharged V6, now chugging at idle, what's wrong?

So the bottom end from my supercharged V6 VY series II seized, and yesterday we installed a 'normal' non supercharged V6 into it. Had a few issues during install, such as EGR valve tube doesn't seem to have an equivalent on the supercharged exhaust assembly so we just blocked the egr valve at the intake manifold end. Also we broke a sensor on the right side (when facing the motor) header meaning that we had to hack together the wiring to connect that sensor to the loom. There is also one 'loose' plug on the right hand side of the main loom near the firewall, it seems to go to a vacuum advance on the supercharged motor but can't seem to find the equivalent on the non supercharged manifold that is in there now.

Had some other issues such as the connection to tailshaft spline alignment, ended up removing that whole rubber connection and reinstalling it back after sliding the mini shaft into the gearbox. Also, installed the linkage upside down (several times!), couldn't figure out why the gears were shifting backwards

Ok, to the main point.... it starts and run pretty decent at high revs, but chugs heavily at low revs and tends to stall if a slight amount of acceleration is not applied. We have tweaked the idle cable a bit but you can tell even at 1000revs that something isn't quite right. Also, the check engine light / warning is on. I'm feeling like it must be on of the sensor connections in the loom that is throwing things out, because we seem to have all the vacuum hoses connected properly. One other thing is that we did a 'join' on the main fuel line into the manifold and perhaps we have restricted the flow a bit.

So... I realise it sounds like a few dodgy things, but I'm pretty sure that just one of those will be causing this chugged. At high revs and high speed it actually goes really nice, it feels smooth and grunty.

Please help me fix the chugging, or it is going to go to a mechanic and $$$... Thanks!

 

A couple of other things: it has new plugs, good leads, good alternator, good battery. New oil, new coolant etc.

 

Ok, this is the memcal/computer from the supercharged version, connected to the non supercharged one. How do we make it right? Does a mechanic have to do this retune with some fancy computer, or can I do it?

 

At this stage it seems the opposite is happening (problems at low revs not high), so does mean it is probably some other issue like vacuum or fuel flow or a sensor problem?

 

How is this done, do you need a special handset to do it or something?

 

So is the memcal replaceable in the VY? I heard something was soldered on but is that the PCM, and the memcal bit can be swapped?

 

Ok cool. So we couldn't have pulled the memcal from the standard ecotec VY donor car anyway? And we need to find a suitable matching memcal, possibly from a VT? Its at mechanic now... wonder if this will cost me an arm and a leg for them to do it.

 

So would a VT or VX memcal work ok in that motor with the VY loom?

 

Or do I need to replace whole PCM? and is that matched to BCM?