As far as sealant, I've discovered that I love the Racing Blue Hylomar --- but it's pricey. A small tube at OReilly is 10 bucks or more. It seals great and also never dries/hardens, thus making it more likely that a future removal won't tear up the gaskets and you'll be able to reuse them. I like the "good" Felpro gaskets with the rubber/silicone sealing beads around the ports.
Clearancing the water pump. Do it - it can make a huge difference in how well the pump works. Lay the plate on the bare pump with no gasket between them, work around the plate opening with a hammer (gently now, Roger) until it just kisses the impeller. Once you reassemble with the gasket in place, clearance will be optimium.
As far as the sequence, it can be a trade off. If you've put time and effort into port matching the intake to your heads (and gaskets) then if you tighten that long bolt first it's going to pull everything out of alignment and all that work will have been for naught. However, if you torque the manifold first it can make it tougher to get a good seal between the manifold and the timing/pump cover - as mentioned. Your call on that one.