Ok,

So my water pump is leaking! Argh! I am gonna replace it with one (probably from stewart components). Since I have to drain the coolant anything else to fix/replace at the same time?

I am gonna do a thermostat change, still deciding on 160 or 180, there seems to be quite a bit of debate on this..I am leaning toward 160, and I can burn my proms (whole other thread about what to change).

I was thinking of ripping out the AIR stuff and pump (since I have to take the belt off, and the air line to the cat is smashed flat anyway.) Any adverse affect to this? Again there seems to be a lot of debate either way.

Anyone have any other suggestions of stuff to do while I am at it?
(Besides a new intake which I can't seem to talk my wife into)

Water pump off is a good time to replace the timing chain and maybe a cam too if you were thinking about getting one.

Winter is coming soon so I wouldn't put a 160 tstat in right before winter. I always run a 195* with bypass holes drilled in it for winter, then just run without a tstat in summer. If you don't drive it in winter then a 160 tstat is no problem since you won't need your heater to work.

Removing the air injection isn't a problem if you also remove or hollow out the CAT. The CAT will run cooler without the air injection and tends to clog easier when the engine is rich. They work better with the air, but if you remove the CAT too, then it's no problem.

Replacing all your coolant lines is usually a good thing to do at this time.

All of the stuff you mention is easy to do even with the water pump on. I would replace the pump/gaskets, upper and lower radiator hose and as for the thermostat, go with th e180. A cam swap is a good idea, but don't decide to do it just because the water pump is off. You'll still be miles away from getting the cam out. you'll also have to take out the radiator, timing cover, intake manifold, drop the oil pan, timing cover, yadda yadda yadda. In the grand scheme of things, the water pump is no big deal.