Maybe you should make a deal with the shop. Tell 'em you'll pay to have this checked (assuming they have the tools and skill to accurately do so) -and if there's a problem, ie. out of spec. they pay for the whole shebang under warranty. Personally, I believe Donny Petersen's 1 thou. spec. -Hell, there's not even a bearing for the back of the cam journal to spin in!
You'll have the satisfaction of KNOWING the pinion shaft runout, and the satisfaction of a smoother ride!
I'd make sure if it isn't within .001" runout, they have someone who can true the flywheels. I wouldn't want some highschool dropout new "tech" telling me the runout is at -say .003" and have them put it back together telling you "it's OK, it's not at .004".
-Just my 2 cents.