In my opinion and suggestion,
1 - You need to keep Coolant and don’t flood Heatant, or the reactor would stop working.
I guess your reactor was stopped because of this reason.
I suggest you use Logistics Tanks to save Coolant and use bigger pipe to transport Heatant.
2 - I don’t know the details, but I guess pollution will be caused if polluted water isn’t processed well.
And it’s difficult to remove pollution, probably waiting so many years is the only way to remove.
Using Lead Block or IC2 blocks to block radiation is the good idea, this function is like Deep Resonance Mod.
3 - We need Distilled Water to get Steam and Coolant.
Large one will be useful stuff.
4 - I suggest high tier machine(Ex. LuV, ZPM) needs the materials which are made by nuclear fusion or fission.