Sounds like a few issues to me. Any mechanical tapping that comes through the speaker suggests one or both of the pickups is microphonic. You can send them here for testing, but you can probably confirm yourself by tapping the pickups themselves and see if you hear a thumping sound.
I would visually inspect the electronics cavity (you can post images here as well) and make sure that the volume control board can't hit the edge of the cavity, which would cause the signal to short and drop out. The cells that are under the pressure of the nut and washer holding the pots in place will compress over time, which can allow the board inside to travel when you reach the stop.
An early Epic, like yours, would have the first generation of the bass and treble pots that do not have an internal wave washer. This makes the pots have a looser feel and also means you have to use plastic knobs like the original collet knobs you described.
It's hard for me to imagine the circumstances that would make the amount of bass decrease over time now that wouldn't have been present from the get go, I mean, maybe there's a failed or failing cap, but seems unlikely.
If the bass was every stored for a long period of time (like a year) the cleaning procedure might not be effective and the pots would need to be replaced. I know you said you haven't played it in a year, but that was after you had the issue, so while it wouldn't be the cause it may have compounded it.
If the sound you are hearing is like a high frequency sound, there is an RF upgrade chip replacement available, but that doesn't sound like the issue you are having from the description above.
Can you post an image or two of the electronics cavity? Also get back with your test results on the tapping the pickups directly.
