Very strange sound but definitely ring / piston / port related. First I'll address some of the concerns.
1.Pistons are not straight. The top ( where the rings go ) is smaller in diameter than the bottom skirt. The largest part of the piston is an area about 1/2” above where the skirt ends and at 90 degrees to the wrist pin. This is the area to be measured when calculating piston / bore clearance. This will always be the first area of the piston that starts to show signs of being worn.
2.Evidence of the hone pattern only being visible on the bottom sides of the cylinder is normal.
Make sure the rings are in the correct way. I'm assuming you run a Wiseco piston. The rings will be marked on one side. The mark faces up. It doesn't matter where you put them ( top or bottom groove ) if everything is new but never switch the position after the engine has been run. Lay the rings on a flat surface and make sure they're still flat and not distorted. Check the ring end gap. It should be at least .011. Just push the ring into the top of the bore about an inch and check with a feeler gage. The ring has to be parallel to the top of the bore to get an accurate measurement. Check the clearance between the ring and the ring groove in the piston. Anything over .002 is bad. You can also measure the width of the ring but you'll need a set of dial calipers. You should find no variation in the width. If you do, note where the ring gets smaller in relationship to the cylinder. Pay particular attention to the thickness of the ring in relationship to the exhaust port. Check the piston / cylinder clearance. This cane be done with a feeler gage if you don't own a bore gage. With the piston and cylinder off the engine, slide the piston ( take the rings off) into the bottom of the cylinder. Slide a feeler gage between the cylinder and the bottom part on the skirt @ 90 degrees to the pin. DON'T FORCE IT!!!! Start with a .001 and work your way up .001 at a time. If a .002 wont go between the piston and the cylinder, you need more clearance. If a .005 goes in, time of a new bore. I typically run .0025 - .004 depending on what I'm doing with a certain engine. Don't even think about re-using the C clip. Check the ring locating pins in the back of piston, if you can move them or take them out, the piston is junk. Take a good look at the chamfers on the ports, they should be nice and round. Pay particular attention to the exhaust port. If you have a loop or magnifying glass, examine the face of the rings. Look for any burrs. This should help but if after all this you don't find anything, give me a call. I'll be in the shop all day. 860-230-5003
Ken