So, I'm looking at either an engine rebuild costing around $4,800 or a new engine costing around $6,200.
I was in this same predicament two months ago. The crank on my '06 CVO Ultra was binding and I needed to decide between a rebuild, or an S&S drop in crate motor. The engine was virtually untouched for 80K miles, never having the heads off, or cams and lifters changed. So I went with the rebuild using quality parts in the key areas, cams, lifters, and bearings. Jim at Metal Dragon did work. I chose the rebuild because it was the less expensive option which allowed me to upgrade to a new 2-1 exhaust system.
Jim knows I do not chase HP/TQ numbers, and that I prefer long distance rides, and police rodeo competitions. So he built me a solid dependable motor with the right cams and tune to give a fun "kick" when I get on it.
Lastly, I chose to stay with the HD motor because of availability. In other words, if I should have any issues on the road, any dealership can work on it. Not to say they couldn't or wouldn't work on an S&S engine.
Mark