I am having a genuinely frustrating problem. I had the exhaust on both cylinders glowing red, after lapping the valves and refitting, same problem, two new exhaust valves lapped in, left hand cylinder seems to be ok, but right hand still glowing, lap valve in again, no improvement, bought second hand head, lapped on still same problem, stripped head again, lapped in valve, checked timing (Lucas Rita electronic, advanced very slightly.) exhaust still glowing, Help, anyone!
Air leaks on the intake side? Inlet stub to head, carb to inlet stub, Airbox/filter to carb all ok? You could try spraying some WD40 around the inlet side joints when the engine is running and see if revs increase.
Any chance valve timing out.
The right hand cylinder sits slightly forward of the left and so the bend is closer to the head on that side. I’m assuming your bike has single skin stainless pipes which are much thinner than the standard double skin chromed steel ones fitted by the factory.
Personally i would ditch the Lucas Rita!
Why? I’ll has been ok for the past 44 years, I fitted it because of the very poor starting of a previously owned T3, which could be a positive pain!
Hmm, I don’t think that is the problem, unless the timing chain has stretched more than a bit, may have to investigate that one.
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Just wondered if engine had been apart it could be. Carburation is my guess, what do the plugs say?
I think valve timing also. A T3 Cali I obtained ticked over lovely at 1000RPM only to find one cylinder wasn’t firing at all. Quite odd. A compression check will discover if valves are sealing , but at the right time ? Assume tappets are clearance. On a Norton I’ve swapped carbs left to right can you do this on a Guzzi? On a Norton you can swap HT leads not on a guzzi as both pistons are not at TDC together . So
Have good compression , is the spark at about 6 degrees BFTDC with both tappets loose, can carb on faulty cylinder be swooped or replaced temporarily think that should eliminate the area of fault. 
happy to discuss
Does it advance ? A Duke SS goes from 6 to 38 degrees BFTDC if the revs pick up but no advance then well retarded ie what’s the affect of spark at 6 degrees at 2500 RPM should be on both cylinders though
I would also want to check the advance. I picked up a 1955 AJS 500 that ticked over perfectly, ran up to 50mph perfectly then struggled to go further. Downpipe very discoloured.
It turned out that the auto-advance was stuck on retarded. It was a wholly different machine when fixed - after 450 miles of wondering what the problem was, whether there really was a problem, and not believing it could start and run so well with no advance (so it couldn’t possibly be the ignition at fault!) - and a lot of dismantling of a brand new carb!
Your fault was originally common to both cylinders so unlikely to be carbs or valve wear, I would think. Valve timing quite possibly but ignition timing would be my favourite candidate. Although it’s now more on one cylinder I’m not sure how lapping a valve in would have such a dramatic effect (or what led you to focus on that as the cause of both downpipes suddenly glowing red at the same time - that would be a remarkable coincidence, I think) and I wonder if you are being misled by connecting an apparent change to one thing you did and leaping to the optimistic conclusion that you’ve ‘got it’. Obviously, I’ve only done this once in my lifetime lol!!!
It would be good to know what happened immediately before the problem began - was there some work you did that could be a possible cause or did it appear out of the blue? It sounds like your lapping valves was a response to a newly appearing problem - there may be little connection between that and the source of the problem and it sounds like you have convinced yourself you are on the right track because it produces a change on one cylinder. But we all know carb problems are ignition really, and vice versa.
It’s an ‘interesting’ dilemma, of course, but it sounds like your partial cure may actually be a red herring.
Good luck - I agree with suggestions of others: WD40 all over the inlet rubbers and carbs, switch carbs if possible etc but from the original problem which has now been altered by your valve lapping, I think you are searching for a factor common to both cylinders: ignition or valve timing are my favourites.
I agree, believe modern fuel burns slower so advance needs to be slightly advanced think Guzzi quote 3 degrees a Ferrari workshop I know of said we set at 6 degrees always initially.
Falcone mag advance 15 degrees wondered how mine went so well ? Mag half speed so I assume one degree on mag is two on crank obvious but not to me. Apparently the maximum pressure should be 10degrees after TDC important on old Ducati bevels as less than that crank life is further reduced. Heard of a chap in Birmingham who has done 93k on an old Duke, remarkable 