Any transmission trouble you read about is a rare case, it just seems like there are a bunch because people usually only post when there is a problem. Some people also don't take as good care of their truck as they should. That will also add to the thread count.
If you need to disconnect your battery it is safe to do as long as the programmer is unplugged. This protects the programmer from getting damaged during an electrical surge.
The only time you return the truck to stock is when you are going to a dealership (and do it days in advance) or if you are plugging the programmer into the computer.
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