I've also been working on adapting the FJ80 automatic trans shifter to work with the GM 6L80 transmission.
It's been done before, and the common consensus seems to be that it's "a lot of trial and error".
I went a slightly different route and made everything I could adjustable, but the first thing to do is to convert the shifter from a passenger side mechanism to a drivers side.
The stock FJ80 shifter pivots on a rod, that then pushes a lever back and forth on the passenger side of the transmission tunnel. To get around this, I removed the shift rod, and used my presision milling machine (A.K.A.... a belt grinder) to extend the flats that were machined on the handle side of the shifter rod. This allowed me to put both the shifter handle, as well as the shifter lever, on the drivers side. I had to cut a corresponding slot in the bottom of the shifter mechanism and the floor of the landcruiser to allow the shifter lever to pass through.
Problem 1 solved.