96 Cabriolet Tranmission Advice

I love my Cab - bought a 96 in 2004 in mint condition with 50K miles. Though I now, perhaps though my ignorance, have a big problem.
When I bought the car, the previous owner said the check engine light was on because of a ECU problem - though he and the dealer insisted there wasn't really anything wrong. He showed me the records and the diagnostics that all was OK with the engine from two dealerships. The dealers said it would be 2k to replace the ECU to get the light off, so he opted to carry on and check the engine regularly. As a result of this I was able to get a good deal on the car.
One year ago I had what appeared to be a tranny malfunction. As I sped up from 10 to 20 mph the rpm would cycle from 1 to 2 K and back down. However, when I got above 2K RPM all was OK. This happened once, and it disappeared, happened again 8 MOs later and was really bad, but then I replaced the battery and all was back to normal. in fact the fuel economy improved.
Now, I am getting slippage from 2nd to 3rd gear in the tranny. I was writing off the previous problems to ECU malfunctions, but I am afraid my car was trying to tell me something. I have been reading about tranny failures and realize I may have to spend more than 1K to fix the problem.
Questions. Could the transmission slippage be caused by the ECU? If not, what could I be in for? I do realize I should have taken the car into the shop immediately when it had the first problem - but it seemed so computer related and intermittent that I passed. If I do have to take it in, what kind of place in the US would be a good bet to get quality german service without breaking the bank?
Any and all advice much appreciated. The car now has 60 K miles.
Another question. From the audi pages it seems that all 96 cabs (mine has the winter package) came with the luxury package which included keyless locks. I didn't get the fob with my car, but highly suspect that I already have the receiver. Can anybody confirm this, or tell me where to look to see if I have the hardware to support a fob from ebay?
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