I'm pretty sure my engine has had this issue from the start, but only recently did it start getting bad enough to tear it apart. I found out that not only were my crank bearings very bad, but the crankshaft fit too loosely into the bearings. At its worst, the crank would just spin inside the bearings without the bearings themselves rotating at all. Mind you, there wasn't that much clearance, with the brand new bearings maybe only about .001-.002" but it was enough to make it run poorly and make an annoying clicking or chattering noise. It also caused my crank seals to prematurely wear out after only about 200-300 miles.
Because My crankshaft was otherwise perfect and nicely balanced, I didn't want to order a new crankshaft. So my solution was to add poor-man's knurling to the crankshaft. Just take a small punch, and in a checkerboard pattern, make tiny punches all around the bearing surface of the crank. This pushes the surrounding area up slightly, causing it to fit tightly inside the bearings. It worked, and I ended up having to lightly hammer the crankshaft to push it into the bearings, so I know it's tight (but not too tight). Everything rotates very smoothly now.
Because My crankshaft was otherwise perfect and nicely balanced, I didn't want to order a new crankshaft. So my solution was to add poor-man's knurling to the crankshaft. Just take a small punch, and in a checkerboard pattern, make tiny punches all around the bearing surface of the crank. This pushes the surrounding area up slightly, causing it to fit tightly inside the bearings. It worked, and I ended up having to lightly hammer the crankshaft to push it into the bearings, so I know it's tight (but not too tight). Everything rotates very smoothly now.