Picked this up a few days ago ... it's an ES & the owner said it had shifting issues & had been sitting for roughly 6-mos to a year. Battery was dead of course.

Got it home and checked it out ... seems to shift through all gears just fine & fired right up with a power pack. However, when idling, I'm hearing the noise in the video below .... what am I looking at, upper, lower, valves, or ???

Does it get louder as you go faster..if it does i would think its the belt

holy cow, thats a toasted rod- or a bent rod from sucking in water- either way its gotta be tore down before it explodes and sends metal into your transmission.

So, I'm looking at an upper AND lower rebuild?

Take the head and cylinder off, inspect all parts for damage, you will probably be able to see if it is in the "bottom end" or just the "top end" that needs work. Honda 350s used to drop valve seats, which made an awful clatter, though not as bad as your soundtrack, so check the seats if the cause isn't instantly obvious.

Finally got around to cleaning (pressure washing) the engine over the weekend; and, this afternoon, I removed the head & cylinder.

No evidence of water / sand in the crankcase. The head looks pretty good. No up/down movement on the rod that I can detect; but, there was some side-to-side (normal?). The piston skirts look bad to me; and, so do the adjacent cylinder walls. Rings look fine.

What do you see (sorry for the one blurry pic)???

Looks like been rode down the highway at high speeds...buy the color of piston and cylinder bore.....if rod and crank rotates great and freely bore cylinder and oversize piston if cylinder will cleanup okay.IMO

Also if you can remove wrist pin and let us all see photo of pin and small end of rod.!

Yes, the gudgeon (wrist) pin has probably seized and the cylinder needs an oversize piston and re-bore. The con rod eye will probably be scored, but careful reaming out should restore it to working order. Most likely cause is running short of oil, but overheating can do it too, so check the fan is working. Take the valves out and check those seats, the noise was awful loud for just piston slap.

Previous owner sold it to me as having a "trans issue" - not cranked in 6-mths or more. I assumed it was ES related & took the bait. In my own ignorance, I took a power pack & cranked the engine before buying & heard the knock clearly - but, knowing it hadn't ran in several months, I shut it off quick & wrote it off as being dry. I didn't get much info outside of that ... it was a teenager.

The ATV was low on oil, and it was dark. No fragments were in the filter. Coolant was full & green - fan works, but can't say if it was coming on properly or if the coolant was actually circulating. There's evidence that the ATV may have tipped on its side or rolled. It was muddy, like most - may have been swamped. Based on the piston apron condition - I say starved of oil, or water got in.

More pics & videos ... note in the video the side-to-side movement of the rod; I can't detect by hand any up & down movement. The rod/crank rotate freely. The piston moved on the wrist pin freely as well; it took a taps to remove the wrist pin after removing the retainer clips, but nothing abnormal - I used a deep well socket. Wrist pin slides in/out of con rod eye freely.