Known problems:-
Oil leak around front bottom left engine mounting bolt, caused by using oversized bolt, usually after fitting engine bars or omitting washer. This is a main oil gallery & may result in scrapped crankcases - VERY expensive! Try a specialist for aluminium welding advice first.
Clutch bearing Honda Ref.264 can wear to the point of it disintegrating, falling into and damaging the gearbox. If there is any play here at all - replace it. Also wear between the clutch basket and primary drive gear, which is riveted to the back. The built in shock absorber springs sag after high mileages, leaving the basket to wobble back and forth on the primary gear. A little movement isn't too much of a problem, but excessive play means a new clutch basket.
The needle roller cage Ref. 265 that sits inside the starter drive gear boss and supports it on it's shaft can fail at high mileages and cause extensive damage. Replace this if in any doubt with later type P/no. 91007-426-004 especially if you have the engine stripped.
The primary drive rubbers Ref.140 of which there are 8 will have to be replaced if there is any degree of free play about the rotational axis. Mine had turned to a hard plastic rather than the rubber they are meant to be.
Quite a few o-rings will also have perished and require replacement. Try the local plumbers merchant first for a cheaper solution to buying genuine spares.
When sealing the crankcase halves, make sure the gasket compound seals the inside edge, i.e. towards the oil sump, of the two non- bolt holes at the front and rear of the engine. Note: parts of the top and bottom halves do not contact each other, mark these areas before sealing compound is applied.
The gearshift selector oil seal mounting hole may be corroded, if so, apply sealing compound before installing the seal, I didn't and mine leaked. After a thorough degrease the seal was replaced with the sealant and I now have an oil tight engine. This was easily done without stripping crankcases or removing the engine.
Noise from the bottom end is usually a worn primary drive chain - replace if in doubt, this is a major strip down of the entire engine.