I bought two transistors (2N5088 and 2N2222) to try in the circuit and think that they sound different. One has more gain while the other has a warmer tone, I forget which is which. I thought about doing the same thing you are talking about here. I think you would need a 3p3t to switch the base emitter and collector between the two transistors. I'm not sure how you would do it with three, I guess not with a stomp switch.
one thing that woried me is the abrupt change between transistors would probably cause loud popping sounds thrugh your amp, at least mine did when I accadentally inserted one into the socket while live. I am sure that this is not good for the amp, and possably the transistor.
I would be interested in the results if you try this, perhaps other people have ideas on how well this would work? I'd love to see a schematic if it involves more than just the switch.