You can do It, give in to your custom sump desires

A couple things I see right off the bat are...
1 - Your lifereef skimmer really should run on its own pump. This is important for maintaining a consistent flow through the skimmer, if it's plumbed into a manifold as your reactors clog up it will change the flow rate, in this case increase, into your skimmer. I would think using one half of the turbine for the skimmer and the other outlet for the manifold might work. You would need a separate return pump which you've already considered.
Understood, but if I have a ball valve on the manifold output to skimmer and lets say its not fully open, would also clogging reactors increase the flow to the manifold output to skimmer?
I think also I will be running it from 2nd output of the turbine though Jeff said this will not be a good idea.
2 - Ideally your one flow sensor will be as close to your return inlet as possible to give you accurate flow rates.
I tried to have like 5 inches before and after the flow sensor to comply with the instruction below. This is 1 inch sensor
3 - your drain flow sensor should be placed above the gate valve and not on your secondary drain for accurate flow rates as this will be your main drain.