One crucial step which may have been mentioned, is to completely clean all cylinders bored or honed in warm soapy water to remove any hidden traces of fine metal after a hone,bore or contamination. Dry it fast and some light oil will prevent the "flash rust".
I also like to chase all threads with a tap, making sure 1.5X the diameter is the length needed for optimum thread strength. For example, those 6x1.0 pitch case bolts need to be 9mm thread length, more is not necessary. I learned this when working with a toolmaker as well as owning my own machine shop.
Check ALL gasket or honda-bond mating surfaces with a fine stone such as a toolmakers stone with WD40 and watch the high spots disappear!! Remove the dowel pins and clean them, then lightly oil them and reinstall them for an easy re-assembly. These issues you may find are from prior owners that smashed mating surfaces apart, and back together. Most motors have a casting "boss" for a brass drift and light

to avoid damage to the surfaces.
I also apply grease to my clutch cover, stator side cover gaskets and some others and don't have leaks; The gasket can be re-used.
It's also time to yank the clutch cover and clean the "oil filter rotor" which is a centrifugal type of oil filter rather than a paper oil filter element such as on your 86/87 250SX. Look at the damage to that top end, that damage all goes in the oil filter rotor and some out the left side steel mesh filter.