I had a similar experience recently; I stripped the engine on my C5 to investigate the cause of increased vibration and noise, fearing big-end failure. In the event, the big-end was ok. Whilst it had a fair degree of side-play it had no up and down play. I sought the opinion of an engineer friend of mine who concurred that it was fine. I replaced the timing side main, together with all the needle roller gearbox shaft bearings and the sleeve gear bearing, which had a distinct rough spot. On my engine there was evidence that the rotor had been rubbing against the generator stator in that some of the segments had worn on the outside. This was with a Carberry plate fitted and I have to say that when I carry out the first service after the rebuild I’m removing mine. It didn’t stop the weak timing side main bearing lunching itself and might even have caused it by holding the shaft firmly in one position. I’m thinking here of how back in the day some manufacturers of vertical twins put in a central main bearing in an effort to cure the vibration apparent on Triumph twins. This didn’t do much good and crankshaft whip turned out to be better than trying to restrain it given that Triumphs seemed to withstand being thrashed better than most. In my opinion the Carberry won’t improve a shaker; at best it’ll shift the vibration of an already smooth (for a 500 single) up the rev range and the owner will mention a small improvement. I’ve never come across anyone who has said that the plate transformed the smoothness of their engine....
Sadly my engine still vibrates, though the tapping/knocking noise has gone. I’m afraid that, whilst probably not that common an issue, the earlier ones (pre Euro IV?) can have inferior bearings fitted. Apparently there are a lot of fake bearings in India and although the timing-side main bearing in mine has INA on it (a decent make), it could be a copy. Maybe that’s what RE mean when they say quality control has improved? Who knows...
You will no doubt have noticed that our host sells improved bearings for these bikes, usually with an A suffix. Hopefully the replacement bearing , which looks very like the original but is a different make, will last longer (I did the rebuild at 6,500 miles). I’m not convinced that the bearing is under-specced as timing side bearings don’t have the load to withstand that the double bearings on the drive side need (I left mine alone). BTW, don’t worry about the end float when you bolt the crankcase together, it will disappear when you tighten the crankshaft nut outboard of the sprag clutch. Just don’t forget the thrust washer on the drive side before joining the crankcase.
FWIW while I was at it (and because it kept me busy during lockdown) I fitted a new piston and rings - the engine had gradually lost its sparkle because of worn rings. I also fitted a Hitchcocks replacement exhaust valve. The originals have been known to drop their head if the engine is run at high speed for a while because, like small block Moto Guzzis that suffer the same issue after around 30,000 miles, the valve head is welded to the stem. On mine I reckon an apprentice did the job as there is a pronounced bulge at the join. The inlet valve is much better. Apparently the Hitchcocks valves have a better profile to aid gas flow, though without tuning the engine I doubt that matters much, but it is clearly better made.
You must be a lot more proficient at stripping and rebuilding engines than I am ( not difficult) if you can do it in a day. Getting the gearbox shafts and change mechanism back in place was a challenge (euphemism) but refitting the kickstart spring was a real PITA, though once I’d borrowed some longer fine nose pliers it was easier.
Good luck.
