These are just personal opinions, mine, many may agree, just as many may
disagree.

If at all possible, car wash , and clean engine bay.

a bunch of small paper bags and a marker, for bolts as they are removed, put
them in a bag and mark them.

Scribe a line around the hood hinges before removing them, or use a fine
point sharpie marker.

Remove the grill.

On the AC, I would have it discharged.  Yes the AC compressor can be moved
far enough out of the way to do it that way, but you are stressing the hoses
and crimps that are over 10 years old, and what if you slip and punch a hole
in the condenser?  course you could put a sheet of plywood cut the right
size to protect the condenser, but removing it makes life a bit easier.

On the water pump, why not put it on before you put the engine in place?  In
fact the more you put on the engine before it goes in the hole the easy it
will be after it is in the hole.  And along with the new water pump, get a
good quality heavy duty fan clutch.  The right one will be about 2.5 inches
thick, square shouldered and about 6-8 inches in diameter with a
thermostatic coil spring on the front.

Replace the motor mounts.

Thin coat of quality gasket sealer anywhere its needed, but only where its
needed.  Don't skimp on gaskets.  For the manifolds, use a torque wrench.
Short handled 1/4 inch ratchet with the extension between the index and
center finger and you wont over tighten the valve covers, oil pan or timing
chain cover crushing the gaskets and ending up with leaks.
If you reuse the harmonic balancer, get a repair sleeve for it so the front
seal doesn't leak.

Get some bolts 2-3 inches longer than the bottom bolt on each side of the
tranny, cut the heads off, thread them into the block, makes lining up the
engine to the tranny a lot easier.  If there is enough clearance between the
tranny and the fire wall, four, two on each side is even better.

when you rent the engine hoist, rent an adjustable engine sling, again it
makes the job a lot easier.

Get new bolts for the flywheel to torque converter, and blue lock tight.

While the engine is out, replace the front pump seal on the tranny.

A polaroid or digi camera is a great tool when you don't do this for a daily
living, after two days the memory starts getting fogged, pictures clear the
fog.  Oh and beer is good, beer is great, but at the end of the day, not
during the job.

Engine oil, tranny fluid, power steering fluid, air filter, oil filter, cap,
rotor, wires, plugs, fuel filter, brake clean, hand cleaner, rags, cat
liter, parts cleaning brush.  couple cans of paint, might as well pretty up
the engine bay before the new engine goes in.  Don't forget collector
gaskets for the headers, or new donuts if you meant exhaust manifolds. New
serp belt, and tensionor.

Make sure somebody is there with you when your working and that they check
on you regularly if your doing this solo, don't want to read no obit.
And of course hand in hand with that is if you don't have jack stands, get
some, never ever trust a jack, life is too short.

Whitelightning

Before beginning work under the hood, be sure to disconnect the battery.
Doing this will assure that you don't damage the computer and/or electronic
components. You will also avoid being shocked.