crackling sound out of right speaker

Best of luck to you with that. Please report back on if the problem has in fact been resolved.

Based on your earlier descriptions, something still seems fishy.

Roscoe, You nailed it. Somewhere there is a red herring.

"Replaced input tubes in preamp and amp.
Although I did notice that the crackling did become less after changing input tubes in the amp."

With the system powered up and making the noise, very carefully move the tubes around in their sockets. Don't pull the tubes out, or even go up and down. Just move them a little bit from side to side. If the noise changes, that may indicate an issue with one of the sockets. If you have some contact cleaner, try that as well.

As ZD suggested, do it on ALL tubes input and power ones. Did you try to contact Chris at partsconnexion? He's the one who built your amps and he could guide you through the points you need to check.

I had one of the tech's out today and they seem to think that the issue is a ground loop of some sort, we found a hum coming from the speakers, unfortunately we weren't able to narrow it down to what specifically it could be.
I also did try to wiggle the tubes a bit to see if any change, but no change better or worse.

On another note, I was borrowing a rogue eighty eight from the same shop and today when I was listening to some music, the amp just quit working.