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Since you have the pan dropped, I would just replace the filter. It's pretty likely that with it lying in the pan, the system is not able to pull up enough fluid and reach the pressures it needs to in order to shift correctly. It will come with a new rubber gasket, and should slide smoothly into place and stay there snugly. Note that the transmission requires special synthetic transmission fluid that is VW-specific, and needs to be filled while running at a specific temperature, until fluid overflows from the drain hole with the overflow insert firmly in place.
Well, there is about an inch and a half between the pickup port on the filter, and the corresponding port on the valve body. That would be over a quart of fluid overfilled.
Check your fuse 1 (20a) and fuse 9 (10a), power supply to the ECM. Make sure you have power to the fuse. I just had one of these last week, replaced the PCM and it came right back, found that fuse 1 had power on one side of the fuse, but was losing connection on the other leg of the fuse- wiggling the fuse I could hear the fuel pump relay right above the fuse panel clicking on and off.