Rick--
The TRBs could be the best part of an Indian engine. No problems from mine in a VERY dirty engine that was new 72500 hours ago.
The fuel system from the tank filler neck to the injector pump should be re-done with a remote tank, good filter, and good fittings and hose. I'm using cross link poly tubing and like it so-far. The high pressure lines usually are good...your's are MUCH better *looking* than normal.
The tappet faces are *probably* not square with the shank. I hold mine vertical in a Vee block and surface grind the faces. It works.
Use a common (but very accurate) square and a good level to check the parralality of the deck to the crank and deck to the top of the block and piston will assure the piston is running up and down a vertical hole.
Did you get George's CD yet? Evidently not if you're asking what to do.