First question, how old is the battery? Old batteries cause a surprisingly high amount of maddening electrical situations. And you may have pinched or cut a wire during all that top end work maybe?
Second, I had issues with mice chewing the harness. I did not have the same symptoms, but nonetheless I had issues. It was very hard to see where they got me until I removed the TIPM. They got the harness very near the TIPM connectors, which are large and directly under the TIPM itself. And you could check the integrity of the connectors as well as where the battery cable attaches to the TIPM. The TIPM itself is not hard to remove for inspection and connector integrity. Not saying this is a TIPM problem, but it is a place to check. Of course disconnect the battery prior to doing any of that.