i have some time to kill...
drain the coolant. shut off fuel pump by removing the plug for it in the trunk left side in the hole. start the car and let it die. disconnect the battery. remove all the connections and hoses on top of the manifold. remove plug boots and injector wires. there's a wire grouping that heads down the front passenger side of the motor with 2 wires on it: 1 going to the AC compressor, other goes to the crank position sensor. remove those 2 wires and feed the cable up and out of your way. use a 10mm ratchet and remove the throttle bracket and cables and pull them back somehow. unbolt the 2 bolts on the EGR on the drivers side. it'll stay use a 8mm ratchet and remove the air intake tube, along with MAF and filter (remove maf and iat wires before). if u have a crossmember brace, remove that. remove the 5 10mm bolts on the plenum. remove the hoses that are attached to them. remove the 2 1/2" and 5/8" fuel lines on the passenger side using a fuel line disconnect tool. remove the rear coolant hose on the manifold. disconnect the front coolant drain hose from water neck. remove alternator and alt bracket. unbolt the 11 bolts on the manifold using a 10mm ratchet. some coolant might drain, dont worry. with a vacume handy, scrap off any dirt and clean the area around the ports on the cylinder decks.
you need to tap for the 2nd coolant sensor. if you have a 99/mid01 manifold, get a 3/8" npt (pipe tap) and a 9/16" drill. gradually drill larger holes starting with a small bit until you get to the 9/16". use teh tap and slowly tap it. if you have a mid01+ manifold (aluminum crossover), just tap in the portion right before the water neck. be careful on this if you do. this is because you need to hold the manifold down somehow, and if you mess up on the tap, you're SOL! this is why i recommend tapping the water neck because if you mess up (especually if you're going it urself), you wont ruin ur intake crossover. i've tapped the water neck and have no problems at all with mine.
install the new coolant transfer tube. remove the 2 10 and 12mm (i believe) bolts from the rear of the drivers side head. if the water pump nipple looks like a metal solid piece, get an L-shaped piece of 1/2" coolant line with 2 hose clamps. saw off the part of the coolant tube right before the bend at the front. slide on the rubber hose and clamp it down. there's only 1 bolt with this new tube so just use that. reclamp the rear part with a hose clamp.
this is where the rtv comes in. if u place your new NPI gaskets onto the ports of the PI manifold, you'll see where you need to use the RTV sealant. i'll upload a pic for you later. mark off where on the gaskets you need to "connect to" when going along the gasket. you need to rtv up to the rubber portion of the gasket to ensure no leaks. use a 1/4" bead for this. then, put the manifold on, being careful not to disturb the rtv that is drying. that egr tube is a pain in the ass, have someone hold it up for u if possible. when its on, make sure u move it as little as possible. bolt it down according to the torque sequence in Haynes at about 24 ft-lb's (it basically follows an inner-out sequence going from side to side with the water neck bolts being last).
installation is reverse of removal. let it dry for 12 hours then start it up. check for leaks. if you do, you'll hear a hissing noise and eventually get a lean code.
this is all i can think of right now off the top of my head. if you have questions, just ask. hope this helps.
also, the shots of the rtv are from AFTER i removed the manifold months after doing the pi install. i removed the manifold when doing the headswap and these shots are from that. but you can see where exactly the manifold ports were positioned.