Agroot
Put an oil filter in the crankcase door. It will quicky collect any rag lint or other stuff left in during final assembly.
I totally cleaned my crankcase and all the bottom end, including painting the block, My filter in the crankcase door is showing 'something' a few paint chips, and a slight bit of some black stuff, but nothing is sticking to the magnets! You can see my door filter under SHIPCHIEF in the coppermine gallery, it's made of 30 to the inch stainless screen. Don't make it as big as mine, I can't put the dipstick in. The majority of the oil thrown around inside the engine is not much wider that the big end of the con-rod, so you don't need to make it fit so close to the edges of the door like I did. Nor does the filter have to be complicated. HOTATER made a very simple one that seems to work very well, and he has pictues too. BruceM also has a door filter and some advice.
I didn't think to clean the insides of the pistons. That was brought up in the forum after I put my engine together.
Consider putting bottom rod bearings on the top, and bottom rod bearings on the bottom, use oil dipper tubes. I have the tubes, but put my engine together before the idea of closing off the top oil holes hit the forum. Read about it using the search function.
I think I have a well put together bottom end, but may do a partial disassembly this summer to get caught up on some of the improvements that have come up on the forum, like sealing the head gaskets, measuring the amount the liner sticks up above the cylinder block, cleaning inside the pistons, match weighing pistons and rods, putting bottom rod bearings on top, measuring pre-combustion chamber volume to calculate compression ratio, etc.
Right now I think my engine runs fine, It just powered my whole house during a 4+ day blackout, and the inspections have been fine. Don't get the impression that I think my engine is bad, I just realize (like you) that these are diamonds in the rough.
About engine speed; Mine is rated at 1000 RPM, and it is just starting to hop around at that speed. When it would speed up after the electric load reduced, it would really get hopping, at about 1050 RPM it was real bad. So I followed the advice on the forum and reduced it to 735 with a smaller generator pulley. Now it's fine and still pulls 9 Kw easy which is enough for me. (I have a 12 Kw head)
Scott E