Bunch of stuff to unpack here.
For starters, there's some general wear and tear / age related work you should do:
Replace the Caps. The large filter caps wear out and dry up over time, and since there were all late 80s/early 90s they're 30+ years old and due for replacement or failure. Should breath a lot of new life into the amp.
Replace the LRDs: These Light Dependant Resistors are used to control the channel and feature switching, activating the EQ or changing channels. They wear out over time as well, and are the cause of most weird behaviour on Studio Preamps/Quads that relate to channel switching not working, drops in volume, sapped tone or gain, etc.
Then some general amp knowledge:
Remember that the volume on the clean channel feeds into the gain on the lead channel. Usually 7-8 is where you can limit breakup on clean but still feed the lead strongly, but you'll have to tease out the balance yourself.
It sounds like some bad tubes were definitely affecting you. IF you look up the manual/schematic you can see which tube does what. V1 is largely in control of the clean, later ones do the lead channel, so replaced tube in the lead channel might give you gain back without affecting the clean. Which tubes to use is hotly contested and debated, and you'll probably jsut need to get some and try. I hear lots of good things about the new Tung Sols though. The SPR ones in the jacket are Mesa's special low noise ones designed for V1 to limit amp noise. Mesa buys tubes, tests them, then brands them. So they know they'll work, but you can save a bit of money buying directly from thetubestore or dougs tubes or something.
As for it killing tubes.. that's strange, most preamp tubes should last for a decade or more, I haven't noticed this.
can't remember if there's a difference between black and grey, but it's minor if anything.
Disconnecting the reverb is just as simple as unplugging it, and can be plugged back in. And I don't know about disconnecting the recording outputs, you could just as easily use the effects send outputs to bypass it.
formerly: Quad Preamp, Rocket 44 112