I am pretty sure you CAN click off buffs, such as Thundercloud and Firestarter... not that any sane person would, but for experimental purposes.
So if you want to really test "proc-less" BLM dps:
Only use F1 during your Fire cycle.
You can transition from UI3 to AF3 using a Firestarter proc, same dps as using a normal (halved) cast F3 from UI3.
When applying your choice of Thunder, click off the Thundercloud proc. Otherwise only use T1, the Thundercloud procs using T1 will not have a significant effect over a 5 minute parse.