Well since I did ask, I might as well update.
The problem definitely seems linked to changing temp, and may be related to the engine running rich rather than lean. I have a fairly strong fuel smell with my exhaust and some white vapor at idle. This makes a lot more sense to me, since I've got the PC on with the "jardine and k&n" tune loaded but I haven't got the pipes on yet, so airflow isn't where the PC is expecting.
The O2 sensor is a good call. I will mention it when I take the bike in, just to verify it's working. My guess is that it IS working, and when it picks up changes in temp and O2 it's shifting the fuel mix to accommodate, but without the correct pipes it's throwing the mix off enough to cause the backfiring and roughness.
Pipes are supposed to come in early next week and I should be able to get them on shortly after. Hopefully I won't do any harm in the meantime.
