To put aside the "why are you doing this? Think of the children!" for just a moment, I will - at risk of a public flogging - answer the OP's questions:
A:
The large breather hose connected to the EGR which makes a T fitting with the crank case breather I was planning on running to a catch can. Yes - good idea? (See red handled pick)
The hole you plugged with your pick tool was not connected in any way to the SAI system at any time...ever. You are getting confused between the 2 large metal hard lines that originally ran across the side of the valve cover. They are completely separate systems: PCV (nasty fumes) and SAI (fresh air!). If you want to put catch can in between that 3-way breather hose and the PRV, while still leaving it connected to the TIP, that's not a bad idea. Just make sure nothing leaks.
B:
The small vacuum line which was connected to the EGR I was going to plug. I'd like to just remove it but I see it connects to the solenoid under the intake manifold. What should I do, plug or cut?
You should plug. If you leave it open, you create a vacuum leak whenever the SAI would normally be active. And vacuum leaks are bad. Just trust me on that one.
C:
Finally, I have to admit defeat and mention that I do not know what the third hose in the picture powers, other than it was connected to the turbo inlet pipe so I imagine it needs vacuum.
The 3rd hose is a metered fresh air supply from the turbo inlet pipe to the Suction Jet Pump. It supposedly helps your brakes work better. I'd suggest you hook it up to the TIP, unless you want to actually delete the suction jet pump itself.
I hope the above sheds some light on the various modifications you dove into there. Good Luck with all that.
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