1) Tape over the rod journals with electrical tape. This keeps the crap out and gives some measure of protection to the machined surface. Also tape up the oil hole for the oil pump.
2) Get a drip pan that will catch all of the stuff that drips out of the engine. Later we are going to flush the bores so there will be at least a couple of cups to catch.
3) Turn the crank so the rod journals are 90* to the bores. This gets them out of harms way and makes it so you do not have to rotate it again until everything is flushed.
4)Pack the area at the bottom of the bores with paper towels, or better yet clean rags. Don't be stingy, we want the entire space between the crank and bottom of the bores full, to catch all of the crap that will fall down there. On TDs take some precaution to insure that the hone can not contact the squirters. On the next one that I do, at am going to cut some closed cell foam to be a tight fit in the bores. That will protect the squirters and keep virtually all of the swarf out of the crankcase.
5) Ream the ridges and blow the swarf out. Wipe the bores out with a clean rag.
6) Hone the bores with as little lube as possible. I used WD-40, but any light oil should do. Try to get a crosshatch pattern, if you can. This can be next to impossible depending on the hone you use. I like a ball hone driven by and air drill. To get a good crosshatch pattern you will need a rather slow drill and rapid up and down motion. I get this by reducing the air pressure to the drill and gripping the chuck with a shop rag to slow it down further and keep the load on the drill even. This allows me to get a nice slow even speed. It takes practice but it is well worth it for fast break in and long ring life.
7) Wipe as much of your homemade valve grinding compound out of the bores as you can. Start with clean rags and end up with TP wetted with ATF. Every bit of grit that you can get out of the motor now is some that you don't need to worry about later.
Remove anything that you had protecting the bottom of the bores and squirters but leave the rags packed in atop the crank. Wipe the bottoms of the bores again until white glove clean.
9) At this point, I like to hose the bores down with a whole can of Brakekleen, getting the top of the block and anything else that might have abrasive grit from the hone on it. When this dries carefully remove all of the rags, again working to keep any trapped grit on/in the rags and out of the motor. The grit is quite tenacious and will hide in any available crack or crevis.
10) Hose down the bores again with Brakekleen, washing the crank and inside of the crank case. Pay special attention to the area between the main caps and the crank. You will have to do some of this from underneath. When you are ABSOLUTELY sure you could do surgery on any surface in there, let everything dry off and proceed to the final cleaning the bores before assembly.
11) Now that you are sure that everything is spotless wide out the top of the bores with clean TP. You will almost certainly find a bunch of gray stuff on the TP where your fingers put the most pressure. You will need to generate a tool to wipe the entire bore with TP wetted with ATF. I use a wooden dowel wrapped in enough foam rubber to be 1/2" (+/-) larger than the bore. Wrap the tool with several layers of TP and soak the TP with ATF. Run that up and down in the first hole and repeat until there is NO TRACE of anything but white TP and red ATF. This usually takes me 3 or 4 changes of TP per bore. I like to conserve time and TP so when I am about to change the TP for clean stuff on any given bore, I also wipe the next dirty bore to get a head start on cleaning it. When you are completely sure you are not getting any more color, remove the tape from the rod journals and assemble the motor as you normally would, being sure to check ring end gap at the lowest portion of their travel.
12) Run the motor for a few minutes (until hot) and then change the oil and filter. DO NOT use Fram filters. They are absolute crap and will run all of the remaining grit through the motor instead of trapping it. Remember that all oil filters have some kind of bypass where cold oil does not get filtered. On some it is just ballooning of the filter housing that lets contaminated oil leak by the filter media.
I would also use the lightest oil that you can find for start up since this will be used mainly to flush out any remaining grit and start seating the rings. I would also not use premium oil for the first few thousand miles. Sometimes good oil will not let the rings seat or at least delay seating for up to 10k miles. I have only seen this happen 3 or 4 times in 40 years but it is heartbreaking to have to tear into a new motor to change the rings because it is burning a quart every 500-1000 miles.