Unfortunately your symptoms dont necessarilly point to a definate tube problem,they could be tube related but to tell you to change all your preamp tubes would not necessarilly be the best advice.I'll try to take each symptom individually and see if I can give you some ideas.
1)Sound fading in and out..... This could be tube realated, could be a power supply problem as well,or as simple as dirty sockets.
2)humming with guitar on zero.Is it there with no guitar in the input?While the amp is humming pull V1 and see if it stops,if not replace it and pull V2,and so on to determine which stage is causing the hum.Again,finding the stage or tube that stops the hum doesnt mean it is definately the tube,sub the tube with a known good one,if the hum stops that is it,if not at least you know which stage the hum is coming from.Could also be caused by power tubes that are not matched closely enough.Can be caused by a lot of other problems that are not tube related as well,hard to tell without having the amp on the bench.
3)Crackling and popping.With the amp on in play mode and volume turned up,try rocking each preamp tube in its socket,if it induces the crackling etc your tube sockets need to be cleaned and re-tensioned.This is also an indication of bad plate load resistors.
4)Springy popping... sounds like your reverb reacting to the channel switching,I wouldnt worry too much about that right now.
5)Amp sounds more bubbly and shrill (like a bass amp) Not really sure what you mean by "bubbly".But if you are saying the amp sounds harsh and cold I would suspect the power tubes could be biased too cold.I see this in a lot of Mesa amps,even when using tubes from Mesa or some supplier that grades their tubes to match Mesa's specs.Even tubes that are "in spec" for your amp can vary from set to set,you have a set that sounds nice and warm,you get new tubes that you think match them and they are actually colder than the previous ones,and sound harsher,more shrill.The only way to cure this is to have access to more power tubes to find the ones that sound as warm as your last set,or to have an adjustable bias mod done and find the "sweet spot" by adjusting the bias.Where did you get the power tubes?Are they graded to match Mesa's specs for that amp?Did you in fact install a matched set?How old is the amp?Any mods or repairs ever done to it?It is kind of hard to diagnose an amp from this distance,but these are a few suggestions I can give you from here.Post back after you try some of the suggestions and answers to my questions and we'll try to take it from there.