Dan and Jason have good advice here. Pinion shaft bushing clearance is very important. A lesson I learned the hard way. I rebuilt the lower end of my shovel and set everything up to the tight side of the tolerances. The bushings in the cam cover "looked good" so I just bolted it back on. Less than 5,000 miles later, and over 100 miles from home on the way to a friend's house in Iowa, the engine quit running. Roadside diagnostics revealed a broken pinion shaft. (Aside to Dan, Rev Tramp was riding right beside me when this happened.)
It was a brand new American made part. I figure it broke because there was too much clearance at the bushing allowing the end of the shaft to wiggle back and forth as the cam pushed against it and the bearings were too tight to allow the flywheel end to move. Anyway, lesson learned. Don't do one bearing without addressing all of them. It hadn't been a problem before because the main pinion bearings were worn also so everything was happily slopping around together.
That said, if your runout at the outboard end of the pinion shaft actually is .0065 as you stated in your original post (which is what made me question the pinion bushing to begin with) then a .001 clearance on the bushing is going to cause the same kind of stresses that broke my pinion. You need to carefully check it before you just throw everything back together again. Where are you located? There might be someone local to you who could help.