Wiring ?'s on 97 passat swap into 91 GTI

I am in the middle of swapping a 97 Passat TDI into my 91 GTI and have caused myself a few problems which are:

1) I am not real sure which TDI I have, it came from a 97 Passat and from doing research here the easy ways to tell are looking at the sticker in the trunk but I already got rid of the Passat shell. Or the other way I have seen involves which turbo and MAF it has but my turbo has been upgraded and the MAF is the one that could of come on different engines. So I am looking for any other way to tell which TDI it is.

2) My other big problem is a big mistake on my part, I did research and printed out all kinds of diagrams and pin-outs of the two cars before starting the swap. When I pulled everything apart I labeled each wire as I unplugged it on each of the two cars. Where I messed up is I didn't label the ends of the harnesses at the fuse box. I assumed with swapping the harness and fuse box over the connections would be obvious. I believe I have all the main harnesses that plug into the fuse box figured out but I am having trouble with a few single wires that have plugs on them that plug into other loose plugs. There are a few that I can find a plug of the same color but the wires are different so do all the plug and wire colors match or just plug colors or just wire colors? There are a few of these plugs coming from the instrument cluster harness.

3) The Passat ECU has a Rocket Chip tune in it and I would like to know if it will need to be retuned with the different intake and intercooler set up in the swapped car? If I change the intake manifold will in need a new tune? Does the ECU have to go back to Rocket Chip for this or can I do it with a VAG-COM?

4) There is writing on the ECU from the tune and it says MAF with a circle and line through it which to me means the MAF has been bypassed, does this make sense? If so do I need to keep the MAF in the car?

Sorry for the long post or for any stupid questions, I read through many pages on this forum looking for answers before asking questions but couldn't find exactly what I am looking for. Thanks for any help provided.

Will

From a 1997 Passat, if you saw it in that car, it was either a 1Z or an AHU. For the purposes of this thread it doesn't matter which. If you were ordering parts to rebuild the head it might, but not for a swap.

All the B4 fuse block connections are keyed. I don't think you could plug something in that didn't belong.

Single wires are such the pain. My advice? Find the other end (fuse block end) of that loose wire, and note which connector and which location within that connector that loose end is attached to. From the description in the Bentley, and an accurate identification of the block letter and location number it can be determined where it should go. Then the other loose end can be found by tracing back from that intended end-user.

Write to Jeff at Rocketchip. He'd be the best to identify what you might need to do to use that ECU as it exists. You can use VCDS to scan the ECU label (engine scan, then in the top right of the screen will be an ECU serial. Write that down to provide to Jeff.
At worst, I have the stock FA program chips that would go with the 1997 Passat as it left the factory.
Wanna trade even for the RC chips you have?
I'd be the winner in that game.

this is a great resource, helped me wire my swap and I barely marked anything.
http://www.a2resource.com/
this is the exact link to the CE2 fuse box pinouts
http://www.a2resource.com/electrical/CE2.html