I just finished up blowing out my cooling o-rings for a third time in as many weekends. I'm getting good at the replacement procedure, unfortunately! I get the o-rings in, warm the bike up to 3/4 hot, then PPSSSTTTT, steam show. I've learned to do the test while the bike is parked, instead of driving it far away to test, YMMV. 
It does seem like the carbs must come out to get the coolant log out. There's not enough clearance between carb syncing screws to get the coolant log past the frame. Plus, visuals are very limited with the carbs in. Like you the OP said, rolling back the boots on the airbox, then zip-tying them, is the big secret to removing carbs. I got some reusable zip-ties to make it easier.
A neighbor wandered by while I was working on it, and told me I need to get silicon O-rings. Apparently the rubber ones degrade very quickly if you get any oil/grease/gas on them...? He said I need to wipe them "with glycerine or something". This thread also taught me about o-ring lube, which is likely the better stuff. Thanks for that tip!
FYI, the first time this happened was after I purchased this bike used. I meant to check the coolant, but never got around to it. Recommended! Mine only had about 1 liter of coolant in it. After blowing the o-rings on the road the first time, I drove her home about 50 miles at 3K rpm with the gauge on the far, far right of hot, and she made it home. With the revs low, and wind in the radiator, and less stopping, she stayed alive. I was surprised, I guess. Once I got the coolant log off, I saw the o-rings were pinched at the bottom, as a result of installation with the carbs on.
Hope this helps. I'm gonna try again next weekend. Wish me luck.
Barney,
did you read the Concourier article on the COGdot ORG site, fall 06 about "Coolant Gremlins"? If not, visit there, register, and read it...
I have to ask again, I tried my damndest to alleviate this syndrome when I wrote it, it was My job as the Tech Editor...., I also note to use fork oil to lube the o-rings, as it is rubber friendly, and still affords a seal swell that is acceptable while not overpowering... glycyrin is not an option, it will swell a seal and pop it out so fast.... well, never mind..... we used to put a TEASPOONFUL of glyceryn in each fork to swell seals, back in the 70's, before good stuff was developed..... get my jist?
use the specified o-rings, they will last the longest, silicone ones will not....the compund is not as resistive in contact with coolants.
you have to look closely when installing the log, and make sure none of the rings is rolling out of position, when you see one doing that, hold everything, and poke the o-ring with a small screwdriver, or wooden probe, to assist in it's positioning, and keep pushing.... this is not possible to see with the carbs, and the intake rubbers, in position..... now you know why I wrote the cautions about attempting this in a 'fast' way, without pulling them off.....
we are here for you, best of luck, be patient, and buy more o-rings..... I bought 2x as many as I needed, (i had 2 Conni's at the time) and have no spares.... heeheheheh
