I find it hard to think a rebuilt or used replacement part would automically be a better choice then factory new.
Having went through this myself (prior to the fully splined mainshaft solution) I would purchase based on warrenty.
You get a 12 months 12K miles on a factory new. If any of the rebuilts get you 12months unlimited (depending how you use your truck) this would be a better deal.
I paid 1800K for a 2000 model year 4500HD that was put into my 96. The warrenty lasted 2. 5 months and I was again on my own.
With what is available now I would have NEVER replaced and just rebuilt.
jjw
ND