when I rebuilt my motor, it had a piston pin that let go, scratching the crap outta the right cylinder, rod crammed the piston up against the head at an angle, then the piston got tore to pieces from being jack-hammered in there.
The guy I bought the motor from had gotten it a few years earlier, never ran it. He was told the kicker was locked up, but ran off the starter.
Yea...right.
So anyways, continuing my first rebuild journey, I had the same question about debris in the lower parts, obviously my piston was shattered, yours is just holed, you may have some fine pieces down there, But with mine, I tore the whole motor apart, and the oil in it was chunky with fine pieces of alum from the piston.
I used a full case of carb cleaner to clean it all out, Bought the (now unavailable) 6th oversize kit from mikesxs, it came with matched piston to cylinders, proper ryko rings.
Had a local shop clean up the head, I put in new valves put it all back together, fired rite up, runs great.
Mikesxs still sells those kits, but they stop at 4th over. If you want to go that route, it may be your best option, being your first rebuild. I learned a lot from this little motor.
You will too.