1987 K100RT.
The bike run flawlessly for maybe 2 minutes and then develops a very light miss that is most noticeable coming off idle. It is similar to an air leak although I have sprayed starting fluid around the boots and hoses with no change in engine speed.

The following have been checked:
Valve clearances
FPR (35 psi at the fuel rail)
Spark plugs (strong spark)
Spark plug wires
Temperature sensor resistance 

What other factors should I be assessing?

Dave

Heresy coming your way : balance the throttle bodies. It's possible you may have one opening slightly later than the others.

Crank case breather hose?

https://www.kbikeparts.com/classickbikes.com/ckb.tech/0.ckb.tech.files/ccb/ccb.htm

With the engine rpm at idle, remove the engine oil fill plug. Does the idle level drop and become rougher? The breather hose is likely not the culprit. Does it stay the same? Examine the hose for cracks.

Idles fine WITH filler plug in place. Idle drops and is very rough when filler cap is REMOVED. What is this telling me?

Also, I want to mention the bike seems to idle smoothly at idle, it is when coming off idle the “missing” is most apparent (up to 1500-2000 rpm at which point it is present, just less detectable). Also, at speed, it seems I feel a slight miss or knock in my right grip which may or may not be related.
Dave

If the idle drops when the filler plug is removed then the engine breather hose is doing its job as intended. Continue your search for the actual cause. 

The engine's internals are pressurised. Any cracks in that breather hose, commonly referred to as a Z pipe, will give it away as faulty. I imagine Duck 'splained that in his post (link) above. I just read the link. It's a good piece for diagnostic of the hose & TB rubber vacuum caps.

Dai,
I checked the throttle bodies using Motion Pro’s SyncPro and the vacuum is about as close as possible given the old gal has original rings and valves and close to 200,000 miles. Also, my understanding is any slight variation between the throttle bodies disappears quickly above an idle - which is not the case.

To (hopefully) assist in troubleshooting my issue, here is a photo of the plugs (1-4). Plugs are relatively new with about 100 miles on them: 

https://share.icloud.com/photos/08aQm1plRcaHLVJI3M_Kx_6lw