I did this a few weeks ago when I took the intake manifold off, obviously the throttle body was off as well. I don't have any idea how anyone could do the job without removing it because as you said, it is tight in there.
The water pipes running under the manifold were not a significant problem for me since I had the manifold off. The only suggestion I have is to try to hold the pipes in place with one hand and try to get the pump out with the other. I wouldn't think that the pipes comming out would be a huge deal other than having a little coolant under the manifold and having a hard time getting them back in the right holes. I didn't get to replace the o-rings because I forgot to order them.
The bottom bolt on the water pump is quite frankly a beotch to get out and back on. I just used a 10mm wrench to slowly turn it out but had a 10mm pivoting ratchet wrench to put it back in with. It takes time and patience but is do-able.
Yes, the system is self bleeding. Refill the coolant, let the car warm up enough for the tstat to open and check to see if you need more.
I'm not sure how much these will help but here are some pictures