Well that only leaves one other possible variable, assuming all the linkage, pivot points, etc. are 100% good to go.
The pilot bushing is dragging on the tip of the input shaft. Think about it, if you feel a grinding into any gear it means the trans gears are still turning. That is the only way grinding could possibly occur. There are two ways to get the trans gears to turn. Roll the rear wheels (or drive shaft) or have the flwheel assembly turning (motor is running).
Because TKO use a very light weight
oil (like ATF) and because they have very little internal friction (compared to a top loader) the slighest drag could cause the gears to keep turning.