74k5,
I made the mistake of putting a bodylift on my old Taco on top of the Fabtech suspension lift. As per the instructions of the bodylift, you're supposed to cut the shifter and weld in a spacer to extend the shifter. After the install, I had the same problem as you. Being a mechanic, I knew someone with a transmission shop and he had some Toyota 5spd shifters laying around. I took a few home, removed the screws that hold the shifter console from the transmission hump between the seats. After this is out, my memory gets blurry, but I think there was something else to remove, probably the boot, then you can swap the shifters. It should shift fine without the extended shifter you currently have. HTH!!