Sounds like you still have some solder joints acting up to find. The last Hot Rod series amp I had with crackling was found on the staked-in fast-on terminals over on the primary/secondary side....where I usually DON'T find the trouble. My biggest complaint on this series is the really poor quality PCB material used. The adhesive under the foil breaks down under re-heating of solder pads while changing parts with the greatest of ease. It doesn't help that Fender folds the leads over prior to flow-soldering the board, so you can't use a Pace Desoldering tool directly. (At least you can on the IC's and relays).
You may still have further damage that you didn't find on the tube PCB's down below. Sounds like you're well aware of the normal solder fractures that plague the Hot Rod Series (input jacks, foot switch/pre out/pwr amp in jacks, pots & their support brackets, the tiny solder-masked pads for the power supply caps (I hate how Fender thought it wise to reduce those tinned pads to be so tiny, and NOT use all of the pad dia as should have be done!). I work on Hot Rod series all the time, as there's at least 20 in the rental inventory where my shop is, as well as with other clients. They do come back together and work fine again. And, there's an easy mod to reduce the excessive gain in the More Drive mode.
If you haven't already done so, I'd scrub the PCB wherever you see evidence of the drink being spilled into it, as that also coul dbe your source of the crackling.