I can see a lot of trash in the bottom end on top hard telling whats down in the bearings, your pics are kind of dark any way to shine a light and get better pics?

Again using your provided picture if I zoom in and brighten it up a little you can see the discoloration on the lower rod roller bearings something causes the uneven color.

Metal fragments stuck to other moving parts like the piston and low compression is your Engine talking to you something is not right. Its a gamble to just flush out the bottom end best you can and try to run it if their is a bearing in the bottom end going bad cleaning will not fix it and it will soon fail, the only way to tell for sure would be to take it apart and CSI the bottom end.

Did you find anything in the bottom end? Sometimes failing crank main bearings will cause exactly whats happening here. If you want to save your cases and crank I suggest you split them open and CSI everything.

Who used a wire brush on rebuilding that Engine?

The cyl needs to be lightly honed but watch out. Since you are already at 82mm you have no more room for a bore - but I'd still try and measure if you can slightly hone it out without making too much clearance otherwise you'll need a new cyl. Please also check/measure your squish bank on the cyl head. You might want to get a new dome for that head also.

I've seen this same exact thing on my jet ski Engine and when I finally split the cases I saw tones of metal shaving and crank bearings falling apart. Sad day.

The good is you might be able to save that crank.