Thanks Ken. I was going to give an update, but I couldn't find this thread. Things are going a little better for now. The manifolds tested fine and I simply couldn't find anything wrong with anything. I put everything back together and tested this weekend. It ran great. No issues with water in the cylinders. No water in the oil. No overheating. I tested compression and it's solid all the way around. My only issue left is hard starting after being warm. I'm hoping that's just some carb adjustments, but we'll see.
I think I'm good there. I've been through several tanks this spring while doing all of the break in and setup. I'm somewhere around 25 hours on the rebuild.