You know I hate GUIs, there wont be any. 
And disabling Slots would be done with Redstone, each Block has 4 Slots so the Mode Selector Cover can easily handle that.
Nope, Heat Exchangers + Boiler it will be. And if you put the Boiler right above the Reactor you wont even need Pipes at all, heck the Heat Exchangers could just dump the colder Coolant right back into the Reactor.
As much as you want, you can even make just a 2x2 Single Block Reactor with just one of the Blocks shown in the Screenshot.
Yeah this Control Rod Concept is what I had in mind in some way. Each Fuel Rod will have properties like how many Neutrons it emits normally, or how much Energy it emits when hit by another Neutron Source, or a reflected Neutron. I am not sure yet how I will math it out, I only made the Reactor Model so far.
As for the whole Heat and Meltdown System, the Reactor is operated on Liquid Coolant already, so no Coolant Cells or Vents like IC2 has, you just need to be super careful about operating that Reactor since you can easily produce too much power, at least i think Iām gonna make ways for too much power at once.
Also what you dont see on the Picture because i rotated it away with a wrench, there is two Facings for those, one that emits Cold Coolant and one that emits Hot Coolant. Easier for Reactor Logistics.
Just for Reference since the Screenshot changes about weekly:
