sure... drill it. dont use an overflow box, they are a flood waiting to happen. i would go with a calfo style overflow, so the tank will be drilled on the back with a horizontal overflow box in the top of the tank for the water to spill over and go down the drain. not sure what the consensus is in the reefing world, but i have about 10X - 15X turnover of tank volume thru the sump per hour (depends on if you subtract for lr and sand). that would mean you will need a pump that does 700 gph after head pressure (for submersible, i would use a mag9). i would also recommend that you have the tank drilled with two holes for drains with each one large enough to handle the entire amount of flow from your return pump, this will prevent floods if a snail or something else blocks one of the drains.

as far as the live rock rubble becoming a nitrate trap, as long as the flow of the water goes thru the LR and not just over it, that should not be a problem. when i build sumps, i have the water that drains in to the first section (where the LR rubble will be) flow under a baffle and then over another baffle to get to the next section. this keeps the water volume in that section constant but allows the water to flow all the way thru the rock.

as far as size of sump/fuge - the bigger the better. use as much space as you can.

calc and kalk reactors are really convenience items. however, they can keep your tank more stable as you start to waiver in your diligence in testing alk/calc and adding buffer and calc supplements (this will be more of an issue once your coral load is high and they are growing)