There are lot of posts like this throughout the forum. They may not get responded to, but they ARE helpful. I saved this information a while back, and last night finally played around with the output "speaker emulation" caps. I tried a number of values, and also played around with the coupling cap between Q2 and Q3, and the cap in the feedback loop. I finally settled on the following configuration:

As you can see, I put quite a large coupling cap between Q2 and Q3 to allow more bass to pass through. Conversely, I've got a very small cap in the feedback loop. I tried many values, from ridiculously large (100uF) to moderate (.022uF) to none at all, but the little 20pF cap sounded best to me. I'm not really sure why - I just went with what sounded best. The 20pF cap has almost the same effect as no cap there at all (more gain), but I liked the tone a little better than with no cap at all.
I tried a few combinations on the output lowpass RC filters. I didn't try 22nF caps - two 4.7nF caps already cut too much treble for my tastes, so I tried changing only the last cap to 4.7n, and that sounded just right to me.
Also, I found that individual JFETs vary WILDLY in gain. I'm using all MPF102s, but the one I've got in Q1 has quite a bit of gain - more than a J201 that I tried putting in its place! I've tried other MPF102s that had so little gain that I could barely coax any overdrive out of the PT. So, it's a good idea to try out a number of JFETs until you find the ones that give you what you're looking for.
I also found biasing by ear gave me better results than trying to get exactly 4.5 volts. In fact, I've got the Q1 trimpot wired as an external control because I like to play with that one a lot.
The stock Professor Tweed actually sounds great, but I wanted to modify this one to better suit the style of playing I've taken up lately. I used to use the PT a lot on the neck pickup or both pickups on my Tele, for a chimey, just breaking up sound. Now I find myself playing a lot of surf, instrumental rockabilly and spaghetti western type music, and I wanted the PT to sound better using my bridge pickup. Stock it was too brittle for that. Now it still cuts some bass, but all brittleness is gone when using the bridge pup. It's got a very nice, meaty sound, maybe closer to a 5E3 Tweed Deluxe than a Princeton. I'm really happy with the way it sounds on all pickup positions now.