Scott,
I know you will be happy with the build the bike runs fantastic, did you decide what compression your going to run the bike at?"
Personally I did not want to mess with "changing" the bottom end to a different stroke. I already have the 124" for all out getting it and I wanted this bike to have more oomph yet stay reliable and dependable for long hauling / touring with a little playing mixed in there somewhere. For that reason I would say to have the bottom end shored up by having it welded and balanced and putting a timken in. You are already tearing it down to pretty much the cases anyhow this would require very little additonal work on your part and probably some really good piece of mind for the future for you.
I didnt do it due to wanting the bike back and completed to do Hotsprings and MV which I ended up not going to /sigh. I think I made a big mistake and hopefully will not be the guinea pig / poster child for Murphy's law.