Chris
I have pretty much the same set up as you - Phase 1 and Canon and Pocket Wizards - mix of TT5s and Plus 2's.
In simple terms the TT5's would not trigger the Plus 2's until I reset one of the TT5's to "basic trigger mode" (I think that is what it was) using the USB cable attached to my computer and the software for adjusting the settings.
Now that TT5 is kept with the two PLus 2's and used with the Phase 1 kit and the three other TT5s are used as a set with the Canon kit.
I am not that happy with Pocket Wizard, but I have so much invested in the system that I have been slow to invest more cash in another system which ends up being just as tempermental.
If you want more specific info on what I did I can go through the process again and work out exactly what I did.
Regards.
mal