I usually dial in one side for cleans and one for leads. I've never been able to get the same channel to do both really well, although they are certainly workable. Same for the Studio and either of my Mk IIIs. This has never been a problem for me, though. My Mk IV does good cleans and leads, but it's got separate tone stacks. I like the Quad better, though, but they're all great.
Sounds like your 395 might need new filter caps, they all do at some point. Mine has plenty of bass even without the deep, but I use the deep for leads. That wasn't the only Switch-Track they made, the Strategy 500 would probably be king of the hill, and the idea is in the 2:90, too, but the 395 is more versatile IME. I've got a 295, too, and a Triaxis+2:90 to compare with, but neither are as good as the 395.
That's so cool that yours are together again! Just the way they were meant to be!