Update. got the PCM back from the programmer and everything checked out ok, so I hooked everything back up and my scanner still wouldn't link. Tried a third scanner that I borrowed from a parts store and it worked just fine. Moral of story; don't use a cheap $40 scanner if you are doing a LS swap.
The high quality scanner was able to read transmission codes which also solved my shifting issues. Changed out the MLPS switch and the pressure switch manifold that the PCM was having issues communicating with.
Tranny now works like i should

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When i had the instrument cluster out to hook up the gauges, it was a real PITA to hook up the speedo cable, so i made this tool out of an old pair of snap ring pliers and some scrap steel:
Made a lot easier than trying to get my hand back there.
Installed a fuel pressure gage too.
Ive been able to put a few miles on Toshi (thats it's secret name) and it has really transformed the truck! I need to fix an Evap code and tie up some loose ends before going to see the smog nazis, then I'll be able to get some real miles on it and report on mileage, fun factor, and anything else that happens along the journey.
