I'm not an expert on all the amps he's used over the years, but I think one that's been a favorite of his is the low power tweed twin he's had for a long time. It was not exactly "road worthy", but I think he loved the tone.
I think that's the tone he's been after with the Cornells, although they're higher powered.
When he toured behind "From the Cradle", he was using what looked like a one-off Custom Shop tweed twin. I actually think that was probably the genesis of Fender's current amp.
I didn't think his MusicMan era was his best tone. I thought August and Behind the Sun sounded a little too processed, but he sounded better to me on Journeyman. I've always loved his playing, and most of it holds up pretty well, but some of the production does sound dated on some albums.
sorry for rambling ...