Gabe,
I believe there are several short comings with the 110's and had hoped that the 09 would deliver a problem free motor. In the Harley form whether built by hand in front of you or at the MoCo, I do not believe you can get a bike that is not going to be plagued at some point with issues. Whether it be cylinder related, piston skirt related, crank / runout related, or heat related. We still havent touched on flyby wire, or clamping force of the heads to the cylinders or the valve train or the cam that delivers 220 cranking compression in a supposed to be 9.3 to 1 engine in reality from most of the checks is closer to 9.7 to 1. The aftermarket can use a cam that lowers the cranking compression and cools the motor, juggs with larger fins for cooling a better piston and heads that have viton seals etc. So I wouldnt even consider having them build it or upgrade it as a 110. If you were to use Axtell juggs with say the Harley 10.5 to 1 piston made by Mahle and a cam that had some reduction in cranking compression as well as having the heads gone through by a qualified pro, you might be happy with the results, but using the stock kit from Harley I just wouldn't do it. If your cases are being replaced before you put the motor back together I would definitely recommend a timken conversion and having your crank pinned / welded or getting a crank from someone like S&S with Timken conversion.
Best of luck look forward to hearing how you approach your rebuild.