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Transmission swap advice needed...

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`Found a very nice 2003 9-3 Vector, very cheap a few months ago. It runs like a top with cold AC, everything works. The buyer is a female contact who knows little about Saabs.
When we looked at it, we knew that it had a bad 5-speed automatic transmission (AISAN) due to water seeping in through the radiator. It’s a famous problem. The previous owner(s) did not get the correct warranty work performed, which happened quite frequently since GM was asleep at the wheel on that one. 2003’s are not found for sale that often now, for obvious reasons.
The car drove only when cold, and I told the buyer that we would do minimal work to it and see what happens. If we did not succeed, I told her we would have to install a replacement transmission, a medium risk repair. The contingency plan was to part the car out if all else failed.
I rebuilt the valve body successfully and installed an external cooler for safety’s sake, even though the radiator had been replaced with a post-recall unit. OK, so it didn’t work, but it shifts well when it does move at all. I tried. “Gearbox Malfunction” is still coming up. Maybe I was too optimistic. The internals are shot and the buyer thinks reprogramming it will fix the problem. I disagree; after driving it a lot, it’s toast.
The problem is the local mechanics. We got a quote for an engine/transmission swap, subframe in/out which should actually have been easier for the mechanic. At great cost and trouble to get the car to the shop and transmission/engine unit shipped all the way from the mainland, the mechanic refused to do the repair when we followed through. Yes, UGH! He didn’t like the idea of swapping the 2003 wiring harnesses and engine processor with a 2006 motor. The seller of the motor/transmission is a specialist and gave us all the details on doing that successfully. The mechanic didn’t care.
We can remove JUST the transmission and swap it out. I have a buyer for the motor only. The local mechanics are highly dramatic, trying to rake her for more repair money than the car is worth, all told. The local Toyota transmission guy won’t do the job but told us a Camry swap is typically about $700 labor, so at least we know what more common cars should cost to repair, a low-side labor baseline.
The real question is “Do we have to reprogram the car to accept the new transmission?” The TCM worked fine before and wasn’t touched. If we move the (few) 2003 sensors onto the 2006 transmission, will the car be operational?
My idea is that the new trans will bolt right up and run. The parts inside the valve body for those years are all numbered the same, there is no computer inside the transmission.
The mechanics we have talked to are so clueless, some of them actually asked if it was real wheel drive. (FAIL) They all want to run a tech II first, start the soap opera going, and vacuum the buyer’s wallet out. I need some comments on the Tech II "nightmare" being peddled. It would be great to hear from some of the certified experts here, if you would!

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