If it's the boot on the back side of the carb that's deformed, you can try taking it out and leaving it off the bike to see if it goes back to the right shape. It's at least free to try.
If it's a rubber boot somewhere else on the air box assembly, I would try giving the part it goes over a wrap or two with tape to take up the space.
If you can't get the parts to seal right, then definitely toss them and get good ones. It's not worth killing the engine to try and save a few bucks.
That's assuming it is actually those things causing the problem. Mine always acts like you describe when it sits overnight. I have to use the choke for a second until it almost feels like a jet becomes unplugged and it runs fine. I've cleaned it plenty of times with no change and just live with it now.
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2001 Mojave- White Brothers exhaust, Pro-Design kill switch, 22x11-10 Kenda Klaws on Itp T-9's
2002 Race prepped Mojave with way more than the first one
1998 Recon
2001 Cat 420D backhoe with a bunch of goodies
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In Memory of Christopher Riley Andrews
1-24-02 to 1-23-06
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