The water pump has two gaskets. The one between the plate and pump needs to seal good. The w/pump to timing cover really needs the ports sealed. I use Permatex High Tach on all my gaskets.

Cleaning the threaded t/cover holes would just need a good tap or thread chaser. Going all the way through isn't a big deal because most all the bolts will have threads extend that far. If it's really bad and not adequate threads, you either drill and install a heli-coil set, or, you hope to get enough thread pressure to seal the pump and put a nut on the other side. Not a real pretty sight, but doable.

If you need to pull the t/cover, don't worry about timing. You won't mess with the chain. The damper will come off (use a puller) and the cover bolts come out as well as the bottom oil pan bolts along the cover and at least one back on the block. Then its a clean and replace syndrome. Stuff some shop towels (paper type are o.k.) between the block and oil pan opening so you don't drop crap in the exposed oil pan. Make sure you use some silicone in the corners at the t/cover-to-pan area and let it set for about 5min. before putting the cover on and tighten all bolts. Get a press to put the damper back on if you don't have one. Pounding with a hammer and block or whatever is a sure sign of ..... fill that in. Then install the w/pump and accys.

Be sure to drain the oil (just in case you drop gasket material while cleaning) after you're done.

Note: replace all the galled bolts and coat the entire bolt with antisieze on reassembly.