Mine ran a little... off... as the rings seated. Not rough though. I had to redo the valve lash as the first time I set it it was too loose and caused a lot of valve noise, but that was easily noticable as the valves we're audibly slapping a bit. If the only variable is motor rebuild, then I doubt the CVT is the cause.
I'd take the valve cover off, check your 4 bolts are tight, the lash again, check your timing right. Theres not much else you touched. I just did the same thing a month ago, only I stayed 57.4. The lash was all I had to go back and do. I didn't have excessive vibrations... it just ran 'right'. It's still waaay tighter but then again, that's just the difference of a fresh higher compression engine and a tired low compression one.
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