switch from oil to diesel fuel. Rinse a coffee can out and put enough in it to get about half an inch over the top of the hone when it's sitting still.
The deisel is easier to clean out and when it runs down it carries a lot of the sediment the stones are scraping off with it.
just make sure to keep that up and down action fast and to not sit still. Also, do your best to not run way past the bottom of the cylinder or you can damage the stones.
other than the little bit left at the top, you are doing fine.
are you having the crank polished and putting in new rod and main bearings?? What about cam bearings?
since you have it that far torn down, may as well do the job right and go ahead put new ones in. Peace of mind!!