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Left looks lean, right is pretty close to correct but a little lean also.

As far as the metal expansion goes, I agree with buddha. In general, the softer the metal (aluminum, copper, gold etc) the farther it expands per degree of temperature. Harder steels, like the ones valves are made of, expand much less. Metal expansion tables are a big part of mechanical engineering.
Every motorcycle Ive ever worked on has had an aluminum head, and all react the same. Its more of the head changing size than the valve getting longer or larger in diameter. As stated, an air cooled motor must be designed to have a much larger operating temperature range than that of a water cooled bike. This is why you see larger valve clearances and more frequent inspection periods with air cooling.
I wish I knew just how far out my valve was, so I could have some reference for you, but I didnt write down how much I ground off. All I remember is it had zero clearance, I ground off the max clearance amount, and put it back in the motor, checked again and it still had no clearance. So back to work I went and ground it again. The motor would still run, but it was very hard to start, and would stall out when I came to a stop (closed throttle) for the first five minutes of riding. I was turning the idle speed up in the morning, and back down once it warmed up. I chased the carbs for a while, but nothing got better until I popped inside the head and found that zero clearance valve.

But, I am off track. Your left cylinder is most definitely lean, so it may well just be the jets in your case. Clean it again, and maybe just replace the jets with new ones. Jets R Us is an excellent source, but I think buddha used to sell them...

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this is true. steel and aluminum will both expand and contract but at different rates. its even more pronounced if youve ever dealt with Ti valves in an aluminum head.
Aaron

The lean condition could be caused by a clogged jet or passage in the carb. The carb itself could be cleaned as good as new, installed on the bike, and a short time later be clogged by a bit of debris that flows down out of the tank, from the fuel valve, or even from one of the lines.
You had the tank professionally cleaned, which is great. And an inline filter is a good idea, but I must caution you that while the filter will keep debris from entering the carb, if the fuel valve is dirty enough it can restrict the flow of fuel enough to cause a lean mixture. Ive personally seen this on a 2 stroke jet ski.
However, I dont think this is the case with your bike, since both cylinders are not even. So yes, check the carb boots, that could be the issue. Also, check for the little rubber cap on the brass tube coming from the left boot. If that is missing, the cylinder could be pulling air through there, causing it to run lean. The right side boot runs all the vacuum duties, the left is just there for balancing the carbs. Its hard to see, and could easily be overlooked.
It wouldnt hurt to pull the carbs again and check the jets out, they are usually easy to remove with a flathead screwdriver, but if gunked up could be difficult to get out. Also, pull the float off and make sure the float needle/seat are clean. If that is partially blocked it could cause a lean condition. You could simply drain each carb into separate cups and compare the amount of fuel to tell if the float needle is blocked.

Seriously no point in arguing all of this until you can verify what jets are in the carbs.

If it has the OEM 37.5 pilot jets then that fully explains the lean condition and everything else. End of story. Just replace them with 40s and be done with it.

If it has 140 main jets in it then those are too big for an otherwise unmodified (stock air box) bike. Put the stock 122.5s back in or a set of 125s if you are buying new. Make sure the needles are not shimmed.

Taking the carbs off and replacing those jets should be job #1. Once that's done you can further diagnose. IMHO it's an awesome idea while the carbs are off to replace the intake boot o-rings unless they were already replaced recently and you absolutely verified it. Other than removing the tank, there's not a lot of economy of effort in checking the valve clearances while the carbs are off but it can't hurt.

I don't know how to say it any more clearly: until the jets are sorted you will not have the bike running right no matter what. Do that FIRST. Once you KNOW what jets are in it THEN you can go about diagnosing other things like vacuum leaks and valve clearances, but with wrong jetting it's KNOWN it will run wrong and you can't fix bad jetting buy adjusting valve clearances or fixing a vacuum leak. In fact you can't diagnose those things until you first get the jetting right.

There MAY be other problems besides jets but you KNOW the jets are suspect so fix that absolutely first.