Hello Steve, I'm long winded but you had a few ?'s sorry.
A few comments from the peanut gallery that I hope helps you a little or at least offer possible or solutions. The clutch.... $hit happens but you have fixed that and the flywheel and also converted to a Hyd. throw out Brg. This package should now be good to go. I choose external slave cylinders rather than internal Hyd TO brgs. My reasoning on this is mostly trouble free operation and if a rare slave failure an external is so easy to get to and it does not take other components with it. External slave cyl. problems are often a result of improper pedal stop or missing pedal stop or the wrong ball stud for fork to not allow alignment. Hyd. internal TO brgs do work well so a matter of choice I guess.
On the engine side the continuous black
oil can be from LOTS of Moly grease used during assembly, it coats bottom of pan for ever it seems but is not a bad thing all in all, hope that is it. Having an
oil analysis done is about 30 bucks and gives great info. Check the net or most truck shops (big rigs) do this on all big rigs so check with them. The constant rusty coolant .... HMMMM ? The absolute way to know if you have a ton of debris on bottom of the block is to find a easy to remove and replace freeze/soft plug near pan rail. Remove the plug to see what is there??? While you have plug out plumb one of those garden hose adapters into a heater hose (install a hose for cleaning if needed) and flush the heck out of the coolant system so open plug dumps stuff out the hole. Then ground wire the block and the radiator so electrolysis does not generate new problems and make sure you run anti rust and coolant with additives to stop any issues.
The engine noise? I would have to hear it but if
oil to lifter was clogged it would show as extreme wear and yours looked good. Get the engine oil sent off for an analysis as they will tell you exactly what metal elements and other particles are in the oil. It comes with a print out on everything and for 30 bucks or so you can't go wrong!!! Hope this helps a little ,if nothing else you might think about all from a new direction turning on a light from something you were thinking already.Let us know what ya find. Jeff C