For fire totems, I guess my approach would be to work out the total damage of the fire totem and the time it lasts for and then apply that as a flat figure on top of the normal rotation DPS, while subtracting a (totem) GCD's worth of DPS for every totem duration interval. So I guess 1 GCD per 60 seconds for Searing Totem or 1 GCD per 20 seconds for Magma Totem. It's not perfect, but it's simple.

I don't think it's worth modelling fire nova unless you plan on adding support for multiple targets.

That's some good ideas and it would probably be quite easy to implement them on top of the current system.
However I plan on adding a multiple target option.

*unfinished thought mode*
Perhaps I can figure a way to calculate a rotation based on the spell with the longest recast. This would need fractional cast amounts of the other spells.
It would break the current dps and clear casting calculations .

I'll probably edit this later on when I have had the time and motivation to think about these possibilities.

2.3.14
Shamanism upgrade
Flame Shock DoT is now hasted.
Updated the Flame Shock glyph
The 4 piece T10 bonus is now handled.
Changed the T8 Flame Shock set bonus.
Removed the calculations where a wait was added instead of casting a LB, when LvB was ready soon. This should speed the things up a little. And the latter was unrealistic usage anyway.

Known Issues
Elemental Mastery is deactivated.
2 piece T10 is has no effect.
Chain Lightning is not part of the rotation at the moment.
Fire damage totems are not modeled.

2.3.15
Increased max number of targets from 4 to 10
Added Chain Lightning support to the rotation
Added Fire Nova support to the rotation
Made Chain Lightning and Fire Nova usage optional
Clearcasting chance correction for multiple targets