I suspect that a ground was mixed up with a positive connection on a connection that was re-connected wrong. The transmission not working right may indicate the problem is there, but the auto box has only plugs that fit one way and the tranny is grounded, case to the chassis. It could also be the tranny just resetting itself with it's adaptive learning ability. Electrical systems specialists are the best at finding this type prob. If you know what electrical connections were recently disconnected during the engine swap, then it will be easier to re-trace the steps for re-connecting electrical items and therefore finding the incorrectly connected item. Electrical systems are not my strong suit but this sounds logical to me...Take the car back to the swap shop and ask them to re-check all electrical connections that were disconnected and make sure that the correct polarity was observed. They should be happy to correct their mistake..I am sure a warranty of some sort was offered on the install, ect.?? Exercise this warranty and encourage them to correct the problem. Run the car by VW to ask the the shops best electrical tech. what he thinks. The service advisor may cooporate and get the head tech up to the drive way to answer your question regarding the plausibility of what I have said here. The advisor may not cooporate, and if that happens just casually stroll back into the shop, back enterance if there is one, and ask any tech who the head or lead tech. is. Service advisors know very little about the actual mechanical components. Some give recommendations and diagnose problems when they are just guessing. The tech. may agree with my assesment and recommend that the swap shop take care of this. It is worth a try to get a second diagnosis from VW. I am assuming that the car is drivable??? A reverse polarity connection eats up any battery very fast.. Good Luck, JK
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