So not much of an update but I got the engine off the floor and on a new engine stand courtesy the Hazard Fraud (Harbor Freight).
Also got access to a BDM tool and got a spare ECU off ebay to practice with, been reading about ecu programming and found a definition file for a 1.9 Jetta (038906016H) which is for a BEW I think.
Its all in German so I'm in the middle of translating everything and copying over the map structures/definitions to my backup ecu file.
I disabled the immobilizer (I think lol), and I'm working on figuring out how to disable transmission related codes.
When I had my daily Passat manual swapped, it was taking longer than expected to get the tune from malone (I think they went on vacation or something), so because I really needed my car by a certain date, I took it early since the mechanical work was all finished and drove it without the new tune (only for like a day or two =P). From what I remember it drove pretty much fine other than the check engine light complaining and the fact that it would rev hang.
I think I'm gonna try to keep the ecu for the truck programmed in the same state as an automatic so that it continues to rev hang and try to change the gear ratios in the software to match the 4l60e for any calculations it needs.
I'm not sure what malone does for standalone ECUs, I wanna say they configure the software as if its a manual but no clue. This will be fun to figure out though =]