[BC_Dan]

If you are suspecting that the metal came from the crank, it would be a good idea to pull the engine and split the case to examine the crank. Adding new pistons to a bad bottom end may be throwing your money away. It doesn't take much to get the engine out of the bulkhead and splitting the case is pretty easy. It's hard to tell from your pictures if the piston is usable, but if it were me and it had any damage, I would replace it. Or both.

 

[BC_Dan]

Porting is taking a die grinder to the intake and maybe the exhaust to open them up a bit so they flow more air. More air means more HP. I would hold off on that until you get a few more rebuilds under your belt

 

[BC_Dan]

Polaris flywheels are well known to be some of the worst to remove. First one I tried bent my medium duty puller as well. I got one from Starting Line Products that was supposed to be stout... and it has been so far I am hoping that I never have to use it again, though!

 

[BC_Dan]

When it comes to the oil pump/water pump drive, replacing the seal takes a special tool. It may be in your best interest to farm that part out, if you don't get it right, you will be replacing it again. Talking from experience here

 

[BC_Dan]

Synthetic is too slippery for break in, it may take forever for the rings to seat. I would siphon out the synthetic and put some regular oil in. The amount that is in the lines and pump should not matter.

 

[BC_Dan]

If it's just annoying, try blipping the choke lever. If it's running a bit lean, that will richen it up pronto.

Congrats on getting it back on the snow!