5.7 TR6060 Starter alignment?

Shipped the trans to Texas Drivetrain Performance. Disassembly showed 3rd and 4th gears got hot, indicating a lack of fluid in the trans at some point before I bought it. Not sure how it was low, there is no drain plug in them. So, paid $2k for trans, bellhousing, flywheel and clutch. Gonna throw $2,700 into it now for new 3rd and 4th gear, synchronizers, input shaft, bearings and shipping.

Definitely would have been money ahead to just buy a complete kit with new T56. That's the risk I took.