Whenever I've seen discussions of punching up the bass on a TS circuit, it's been via that 0.047uf cap in the opamp feedback loop that you already changed. I'd agree that the 0.02uf on the input buffer is best left as is. BTW, if you still want a bit more bass, you might want to try a 0.15uf cap where that 0.047 was.

Can't hurt to change the buffer trannies, though the pinout on the MPSA18 (which is what I've used in all my TS clones) is different, as you mentioned. Just leave the legs a bit long and bend them around carefully to avoid contact between them, and you shouldn't have any problem. I recently did the same thing to change from higher gain trannies to mid-range ones in another distortion pedal, and it worked fine. I'll be interested to hear if you discern any improvement from the switch.

FWIW, my favorite opamp in that circuit (and I've tried a LOT of them) is the TI TLC2272ACP. Seems to strike just the right balance of fidelity and low noise without sounding too antiseptic. Some people swear by the Burr Brown OPA2134A, but I found it a little too hi-fi in that circuit; sounded a little lifeless to me compared to others. But I have one in my MOSFET-conversion TS clone, and it sounds great in there. So go figure....