On a rebuild the first thing you must do is take it apart and inspect it.
Since this engine was nice and clean we were able to dig right in.
As you disassemble you will notice various problems that cause you to look at other items more carefully for damage as well..
This engine had a new top end installed fairly recently as far as hours go.
Unfortunately it was not done correctly and there are many problems with this engine.
Note on the pic below how the base gasket was sucked in.
Instead of removing the cylinder and replacing the base gasket the previous builder filled in the gap with some orange sealant

So you disrupt the smooth flow of the fuel air mixture with a gasket flapping around in there and probably had a air leak making it run lean.
Watch this video and see if you see a problem.
https://www.youtube.com/watch?v=qsK1umAFyUY
Yup.... All bad....
Now, take a look at the pic of the piston below:
What caused that on a recently installed piston?
First off note that the scoring is on the intake side of the piston.
And, there are actually two scoring marks spaced evenly and symmetrically on the piston.