As for valving;
If you're talking about restricting the drain pipes with valves, ya there's no harm. This is how you balance your overflow.
If you mean restricting the return side of the pump, some pumps won't last as long with restricted back-pressure.
My overflow can't quite handle my return pump ( drain design issues ), so my main drain gate valve was a waste of money
I installed a Tee with a ball valve to regulate my return flow. The Tee is
after the pump, so there is no restriction at all
This is what mine looks like ( on the right )
For pumps;
Mag drives are somewhat noisy and create heat
Eheim pumps are great and you could probably get away with a 1250, but don't go buying one yet. It's listed in the Head Loss calculator, but ...
Post your estimated plumbing info and hopefully someone with a similar experience will help steer you in the right direction. I don't want to be the only one recommending it
For a 40g breeder, IMO, 400g/hr is lots
Others may say different, but I'm targeting just over 600g/hr for my 75g
The total flow requirement for you tank is a combination of internal flow and return flow.
The return flow needs to be low enough that your skimmer can do it's job.
Hopefully others will chime in with exact #s for you