I was tempted to respond last night but saw you were getting plenty of help.
I never heard of Pontiac cam/crank timing alignment problems. Is he talking about degreeing the cam? Even if it is out a bit it does not sound like you are looking for a race tune. For a driver you can just install the cam straight up and be done with it, definitely not worth paying extra money to have someone degree it. And I wouldn't worry about the cam bearings unless you suspect a problem- cam bearings are not typically a problem area. It sounds to me like the shop just wants to do a high-end job and make extra money.
Changing the cam in the car is easy, I have done this several times. As already said you just have to get the radiator(s) out of the way. If you don't want to do it yourself you should be able to find a shop willing to do this for you, though you would have to pay for the extra work involved.
Getting a little water in the oil pan is not that big a deal, although should be minimized. In addition to raising the back when draining I have lifted the front end when removing the TC cover which tilts the engine back just a bit. I never thought about sucking water out using a wet vac- worth a try.
Pack a clean rag in the oil pan gap when you get the cover off and clean up the old gaskets from the surfaces before going any further. At the end of the job you will still have to clean up little bits and pieces of junk that get down there. Then flush it out with some oil as already mentioned.
You didn't say whether or not you have ever installed a Pontiac cam before. If so then you know the drill and if not then you can get more good advice here. Just curious- what cams are you considering? Never heard of one that cures "stinky exhaust"
Walt