My rotation tends to go as follows:

Blizzard III --> Thunder III --> Fire III --> Fire I (Fire III when Firestarter is up) --> 504 MP (this is the magic number) --> Blizzard III --> Thunder III~

Every 180 seconds, you can change into another variation...

Blizzard III --> Thunder III --> Fire III --> Fire I (Fire III when Firestarter is up) --> 504 MP (this is the magic number) --> Flare (Swiftcast)>Convert --> Fire I (Fire III when Firestarter is up) --> 504 MP --> Blizzard III --> Thunder III~

Flare can be very useful in rotations, just only when Convert is up to immediately continue DPS. When you have the perfect Piety stat, you will be able to Convert directly into a Fire I and lead up with Blizzard III and Thunder III. In some cases, you have to downgrade for Thunder II until you have the ideal MP (yes, it exists for us BLMs). In regards to your Firestarter & Thundercloud issue, use them when you get them. For Firestarter, I will jump out of a Fire I cast in order to use the Fire III cast (you will jump cancel and immediately be able to Fire III in mid-air, not hurting your damage). For Thundercloud, I wait until my cast finishes before throwing it out. Thundercloud being wasted is a shame, but Firestarter going to waste/over-writing itself hurts far more, in my opinion.