You're correct that the two channels do not use all the same tube stages - and that the clean channel uses less. Each 12AX7 has two tubes in the same bottle.
V1 A and B halves are used by both channels
V2A is only used on the clean channel
V2B is only used on the distortion channel
V3 A and B are used only on the distortion channel
V4 A and B are the FX loop driver and return (both channels)
V5 is the Phase Inverter (both channels)
So if the clean channel is working and the distortion isn't (and if it's a tube fault, not something else), it can only be a failure in one half of V2, or either half of V3. In particular, V3 is a cathode-follower position and this is quite hard on the tube; some preamp tube types, including a lot of the Russian-made ones, have a high failure rate in this type of position, so I would immediately suspect that as being the most likely cause. Try to avoid using a Russian tube in this slot if you can.
If you didn't keep a note of which tube was which, try the old tubes back in the amp one by one to find the dead one, and keep the others as spares, you may need them! If you're not sure where the tube was made - it's often etched on, with the Russian ones, but can be hard to see - have a look at the plates, which are the grey box-like structures inside the tube. If there are two bright chrome strips across each side of the tube, outside the plates, then it's a Chinese tube. If the plate is a fairly rounded shape with a vertical 'dimple' in the side, it's a JJ (Slovakian). Anything else, it's probably Russian - at least if it's a modern-production tube.