2004 Polaris RMK 600 - Metal chips in cylinder

Hello everyone, I am new to the forum and snowmobiling. I recently purchased my first snowmobile, a very used 2004 Polaris RMK 600. I have been running into a problems and looking for answers led me to this forum. I originally bought this for ice fishing but then started to be more interested in snowmobiling. I am hoping some of you with a lot more experience than me could help me trouble shoot and see what ideas you have.

The first time I ran the sled it died a few miles in, turns out the carb bowl trap hose was bent which led to a crack and fuel loss. I fixed this and took the opportunity to clean the carbs. In doing this I managed to break off the fuel screw needle tip, unknowingly. I rode the sled about 40 miles or so in this condition, until I realized what I had done and had to get a different set of carbs from a similar sled.

The sled also had no top end power, both the exhaust bellows were torn. I replaced these and cleaned the valves. I noticed that one of the valves threads were completely stripped from the nut that holds the bellows, so I replaced that valve.

After fixing the exhaust valves I went out for a quick ride. The top end problem seemd to be fixed, but I did not get very far. My sled died and I could not figure out why. After getting a quick tow to a nearby parking lot I continued to try to start my sled. I pulled it a bunch of times, with the throttle depressed a bit for a lot of them. Then I noticed the main wiring harness connection was loose, the locking clip was broken. I pushed it back in and then the sled started up and ran for the mile back to my house.

The next morning I smelt a ton of gas in the garage so I pulled the plugs and turned it over. Gas shot all the way to the ceiling out of the mag side spark plug hole. While cleaning this up I noticed metal shavings! I was thinking they were the threads from the exhaust valve, but I checked with a magnent and they are magnetic. The valves I have are aluminum, the bellows nut is as well. This led me down the path of taking the head off for inspection.

The mag side piston head has some mashed up indentations and there are some really fine particles pressed into the mag head but it does not seem to bad. From reading other posts, it appears the steel is likely crank bearings or seals.
Looking into the crank from the mag side I did find some fine steel pieces, but I was thinking based on the size of pieces that may have passed up into the cylinder that I should be seeing a lot more visible damage indication if it was a crank bearing or seal. The biggest pieces were the ones in the cylinder, the ones in the crankcase were much smaller - I would think there would be a lot more in the crankcase if that where they were coming from?

My main goal is to figure out what the root cause of this is and what damage needs to be fixed so I dont end up continuing to damage the engine. I am thinking there was probably a lean condition from when I had the pilot circuit plugged....not sure if that caused this problem or if it is just a coincidence. I took some pictures, the mag side piston was much lighter than the PTO side piston, I am not sure if this was from running lean or having gas sitting in it cleaned it up?
EDIT: In these pictures I had already cleaned up the mag side piston head, it was a bit lighter than the PTO side but not this much.

I dont want to split the crank case if I dont have to, but it seems like maybe thats what needs to be done. I would really appreciate any advice or ideas anyone has. The couple rides I did get in were enough to get me hooked on snowmobiling, and I want to get back out riding!
My dilema is that it looks like it would be about 200 bucks or more so in tools to get the primary clutch and flywheel off, and if the crank is bad im not sure if it would even be worth replacing at this point.

Thanks for reading and thanks in advance for any ideas or comments! Looking forward to learning more.

Peter