Not likely. If a pot crackles and pops when you turn it, it means that either pot is dirty, or that DC voltage is leaking onto it - which means that a cap must have failed in this case since neither side of the pot is directly connected to a tube. Tubes won't be the problem with the large difference between the channels either - all the tubes are in use all the time on both channels. It probably won't hurt to try changing them, but it's unlikely to fix the problem.
I find with my Tremoverb that how close you can get the channels to each other depends on what settings you have and what you're aiming for - with some settings (mostly the tighter, less bassy, crunchy Marshall-like ones) you can get it very close, to the point that you can switch back and forth and not really be able to tell which channel you're on. With others, less so, since as mikey said the problem of both presence controls still operating on the Red channel affects the negative feedback.
But if the channels are really *substantially* different no matter what you do, there may be a switching LDR out in the parts of the circuit that control the channel cloning - my Tremoverb was like that when I got it, the Red channel would not properly clone to vintage so it remained sounding very different. All the pots on it were very crackly too, and it was simply a matter of contact cleaner/lubricant to fix them.
