Biggest problem is that many mods, including Thaumcraft and Immersive are unfinished. And Thaumcraft in particular was abandoned by the author, so it's not clear when, if ever, missing parts such as Harness and Eldritch stuff will be restored.
Here is how regulating with comparator can be done and a couple or reactor designs that use it.
They have enough cooling to run Thorium at about half speed (i.e. half time they are switched on, half time off to cool down). Efficiency of second design is 558%, first one is four...
Btw, do not forget that you have to use redstone comparator for measuring temperature. I have forgot to re-place it (after previous have fallen in fight with exploding IC2 capacitor) and thing did not go well after that.
Yes, reactor temperature.
Regulating temperature with redstone is not that hard, actually. Reactor emits signal with strength proportional to temperature. By making redstone line before inverted longer you can make reactor float at certain temperature range.
Idea : Make different blocks behave differently depending on temperature. Some can be destroyed at lower temperature than other, or change into other block, or change behaviour. Especially fuel chambers can react differently depending on fuel. Such as giving more energy and head with higher...
Ender Dragon is supposed to be killed with vanilla gear, so no wonder Botania boss is stronger.
Though, in 1.8 even Gaia was easy, if you stack enough buffs from potions and beacons. But I have heard some of potion effects were nerfed in 1.9