Andy,
You REALLY need "the book" for this. The factory service manual will much more specific than the ones you get at Advance or AZ.
The intake does need to come off. The water pump does not. There's a 5/16 bolt protruding from the the front of the intake, with a "clamp" at the water pump. Loosen the bolt (you don't need to remove it), remove the 10 "side" bolts, and the intake should lift straight up.
There are 10 head bolts. As others have said, one row under the valve cover, one along the spark plugs. Note where any "studded" bolts may be, as they must go back in the same holes.
Under no circumstances, should you try an "EZ-out" extractor to remove the broken bolt in the manifold flange. It WILL break, and once a drill bit or EZ-out is broken off in the bolt, it is a NIGHTMARE to remove. You may be better off just taking the head to a machinist. And don't be afraid of HeliCoil thread repairs. When properly done, they're stronger than original threads in iron.
Clean and dry is how everything needs to be for reassembly. The valley cover to the gasket is the ONLY place "glue" is needed for this job. No glue on the block "side" of the cover, thank you. No glue on the intake flange, either. Use the alignment grommets provided for the intake. Head gasket is also clean and dry. If using a common fiber head gasket (Felpro, Victor, etc.), no "retorque" of the head is necessary, either.
Use a wire wheel or ordinary "scraper" to remove the old gaskets. DO NOT use a "ScotchBrite" pad on a drill...
Have fun and be careful!
Jim