I took my Rosie onto a dynamometer - now for me to pay good money for someone to rob me like Dick Turpin but with a rolling road, I had to be desperate.
I got the guy to put her up, and before I say what the results were, let's just hear what he said when I asked what they meant, because it's why it is so hit-and-miss to rely much on the colour or condition of spark plugs, when you have a serious problem:
'It could be either too rich or too lean could be the problem, we won't know until you pay us a fortune to p**s around with your bike, probably breaking and damaging stuff we don't care about and have nothing to do with the problem, your bike is an old POS anyway and it's not as though anyone gets attached to these mobile meccano sets is it...'
Okay, I may have paraphrased the last 3/4 of the statement, but you get the idea - it was extremely unhelpful. I learned that my bike has a dip in power on the particular day and climate (I ain't saying 'climatic' again) the Dyno test was done. I have the graph. I may edit and post it, but it's got a BLEH in the middle instead of that nice curve, and it's ALL below the standard curve I have to compare it with. A bit of a case of fifty bucks for so what.
Of course, worse than not discriminating at all as to whether it is a lean problem or rich one, there's damn all about the 'dynamics' or changing situation as the throttle is cracked open low down.
To be pithy - the biggest issue I noted riding was at exactly overtaking speeds on cool summer (great) evenings, was the engine would cut out as I pulled out to pass a vehicle. Dangerous. Later, as I improved it, there was the cracking open of the throttle while taking away from standing that the engine cut out at, unless I wrenched the throttle wide to the stop!
Now, the relevance to your spark plugs. They are NOT terribly useful in this particular problem, necessarily. My bike, the trouble was Yamaha had LEANED the mixture by putting in an almost-straight jet needle practically having no curve, and the pilot jet was a size too low (at my altitude of normal use Radare!). I used these two items then, the jet needle just one notch LEANER with the clip, from the Dynojet kit I bought for $100 or so, and paid separately on ebay for #20 jets to replace the standard #17.5 that were on mine. Incidentally, the BORE of the carbs, really only means that the engine breathes easier higher up the rpm, it's not a mega-game-changer, the Eliminator 750 I had, used the same carbs and every internal part, as the 900, and had no issues at all that I could see, it was like a damn jet turbine. to the point of boring. Makes you miss the rumble we get on the Seca II / Divvie at 5000rpm is it?!
Yet, the plugs were showing RICH. IE sooty. That's the problem. Misfiring, due to LEAN carburetion, means the cylinder fires only every second time it's meant to let's say, cause enough fuel has hung around from the previous intake stroke and wouldn't be enough gas or petrol in that mixture inside the cylinder to ignite and burn. Yet, that is meant to indicate too RICH !
Hence the plug check is potentially useful - but actually isn't in this case!
My stumbling block was that my usual policy of taking as gold standard that the manufacturer did not make mistakes in the factory. Yamaha did. Your problem is that too many cooks have spoiled your broth, OR you've taken the bike out of the climate and altitude it was happy at. Or both.
There is one golden rule of problem-solving you need to know: if you fiddle with something and as a result the symptoms change, that is progress. It aabsolutely points an arrow to the cause, and thence the solution.
The only issue with blasted carburation is that if you change the altitude or work on the bike on a different day (!) then with borderline mixture problems, are a moving target. you don't know if the change is due to your actions or climate/altitude. So don't mess with it at Grannie's beach house, get it good, then back to North Carolina and expect it to be fine tomorrow, as Radare has pointed out!
One other tip - intermittent problems are the worst. People will charge large sums of money to fix these and NOT manage to do it. Professional mechanics only get it working, then pronounce it fixed when it runs ok. That declaration takes place at a few seconds of time, and I would never trust any but the best to do better than me with such problems. Ringing telephone - it stopped happening, oh hang on, it started happening again...
You are doing a ground-up complete carb check, ensuring all jets are correct and all float levels are the same, and all that, before you even think of much else. Establish that baseline, before worrying about Valve clearances, which are only an issue if they are too tight. they only get too tight in practice with the valve heads or the seats they bang up against, are soft or very worn. I only knew one bike where a manufacturing defect caused this, most engines the gaps open up. (Kawasaki GPz 750 engines also fitted to Eliminator 750, which I had, so I just set the clearances to plus 50% then did not need to adjust them more often on those dodgy exhaust valves that got fitted).
yamaha have no such tendency on these bikes to do this as far as I know. Here's my final word on valve clearances and mixtures - if you start the bike and there's a load of tapping and clanking which reduces as it warms up, I would normally say the clearances are alright. Your problem is, you have not had the bike running properly yet, so it is not as easy to rule out therefore it was right that someone points these out.
TBH it's not necessary for you to FIX the clearances, only measure they are bigger than required. Slack or too big, is fine in terms of mixture, compared to the seriousness of the issues you are having. Ford engines for example, are reknowned for preferring to be clackety. Clackety means no damage gets done! Too tight, is when the problems start ie over-enthusiastic amateurs messing.
So, stone cold, you can take the tank off, and pull off whichever engine cover to turn th engine slowly, find a guide to doing the clearances MEASUREMENT. You don't need to fix them, and just measuring means you could later buy EXACTLY the correct shims you need, not like me buy a bucketload from abroad, then customs open the package, then slap on a tax, then you get them 6 weeks later after paying the Government and Post Office ransom...Jeez, this is why you guys just got fed up being run by His Majesty.
So I got the shims, and there are 40 of them I think. EVEN with that, I barely managed to find some to fit to get the required clearances AND still had to re-use a couple to get that far! No, the measuring exercise will not be wasted and if you take care, you won't even need a new rocker cover gasket.
We keep calm and carry on, is the phrase that especially at this time (re London and Manchester) is the spirit you need, and you have got the persistence. As an ex-teacher, I can say, it is acknowledged the difference between great performers academically and everyone else is, they just seem not phased by failure, they persist. It's just another step and a fail is as good as a win if it eliminates one more option.
Rudyard Kipling I think, must have encountered carburetion problems and figured out to treat triumph and disaster as 'imposters just the same'!
I checked the temperature with the IR thermometer and I discovered that the first cylinder has the same temperature of the others (150C, just a bit low, with the default setting of the mixture); I played a bit with the mixture screw and I felt the cylinder respond to the differences on the setting!