Reusing OEM nuts on a stock engine is OK, for sure, done it a hunnert times. Using stock nuts on HD studs works too, though my built motors have never been as built as some.
On current motor (888 with mild cam) I love the HD nuts supplied by Mike Rieck (Kibblewhite?). They don't need any clearance, are 13mm hex with a broader flange and slightly taller than stock. Gives a really good feel.
I used the protocol I got from Ken at CycleX to tighten the nuts: Take down to x+ torque, then release. Then take down to x++ torque, then releasse, then take down to torque x+++, then release, 5 times. Each iteration brought the nuts a little further down the stud. (APE studs). The final brought the threads to perfectly flush with the top of the nuts, very nice. I ended at 20ft lbs.
Ken says this "burnishes" the threads together, making them a matched set per nut. Makinig up for manufacturing tolerances.
I think I have pics if anyone cares, probably in build thread below, back to the summer.