Just an observation, but the bottom case main bearings show wear, they are worn through to the copper layer. The clutch basket is sometimes lose and would make a noise in neutral with the clutch out, that noise going away with the clutch pulled in. Primary chain often makes noise as well. The window on the shifter should be enlarged as per Honda TSB for a lower chance of missed shifts/possible popping out of gear. The exhaust valves should be checked especially on the inside cylinders. Might make sense to build a bigger motor now on your cases with a 900 crank/and a bigger block (1000 and 1100 blocks had better cooling fins)
those are desirable factory "sport kit" (in US, standard in Europe) rear sets, there should be a corresponding throttle control with the cables coming out on top.....another desirable piece if you have it.
CB1100f.net is a great resource for you build.
I may have an old beefy ATK aluminum swing arm for that bike. If you want me, I will look for it.