So will leaky rubbers going from the airbox to the carbs cause bad running conditions?...
Yes
My first thought was that the carbs will just see a little more air, and this could be adjusted out somehow. But after talking to some folks it seems that if each carb has a different flow it can really mess you up.
yes
My boots are cracked and I think air is getting through.... Cylinder 1 has the worst cracks and it has been cutting in and out lately. Would a leaky airbox to carb boot cause such a problem?
yes
Is it worth 65 bucks to get new ones?
yes
What about replacing the whole setup with pods? I have heard very mixed reviews about them... Is it possible to ever get a bike running well with the pods? Just a matter of re-jetting or is it a bigger pain then that.
yes. If you know what you are doing and have access to a dyno, it's not too much pain. Dental work is pain free with the proper amount of novacaine.
With factory air filters running about 30 bucks and the insulator boots costing 65, it seems the pods and a re-jet might be cheaper?
Add the cost of the jets (several sizes), and donate your considerable time for free (instead of being out joyriding), or add the cost of dyno rental to that $30 pod filter outlay.
Any thoughts?
Oh, yes, lots. And there are many threads where I've typed them out for all to read!
Some of the threads mention that rejetting for pods is fun! But, not many.