2003 fxdl clutch

I have a technical question.

Last Year I had my primary apart I noticed a clutch hub wobble.
Since I had it apart recently putting a 84 tooth ring gear on I checked the
run out on the main shaft. I noticed it was out .005 to .10.
I called a transmission rebuilder in Ohio and explained what I had found
asking him to quote rebuilding my tranny and putting a Andrews main shaft
in.
He told me to save my money due to the fact that almost all of them are out
of tolerance.
It shifts fine and the clutch works perfectly and probably has been like
that since it was new. Have you run across this before? I already purchased
a 5 speed with 1000 miles on it and it is sitting on my shelf in the garage.

Just some input would be helpful before I tear it all apart or do you think
I should wait till I really need to.