Since I couldn't take my computer out to the garage, I printed off TMC's instructions, which were vastly better than the Haynes manual. I went right through those, checking things off as I went. I probably represent the more casual mechanic, as if it can be dropped, broken, or misassembled, I'll probably do it. I add a few suggestions below and a NAPA parts list.

This is a long tedious repair, but it is within the capability of the home mechanic. You just have to be patient, stick with it, and know when to take a break.

TIME FOR THIS REPAIR:
If you're doing this for the first time: Considering the "stuff happens" factor, that old fittings and wires may break, and that you may decide to do things like get injectors ultrasonically cleaned by a shop, figure on having the car down for several days or a couple of weeks/weekends.

COST: I ended up spending around $250 . The guy at NAPA said I saved about $1000 by doing it myself.

PARTS/SUPPLIES NEEDED You may be able to get everything from NAPA, but I did get the heater pipe o-rings from the dealer.

NAPA: upper and lower manifold gasket kits (includes o-rings for gtp, and permatex/RTV sealant) MS95809-1 AND MS95812
heater pipe elbows with o-rings: 660-1736
valve cover gaskets VS50080R
thermostat and seal 215 and 1077
injector o-ring kit 2-12093 (need six of these)
Drive belt? If it's old this is a good time to replace

MISC:
permatex thread sealant
parts cleaner fluid
purple nitrile gloves (best gloves I've found. I can only find these at WalMart for some reason).
scotch brite pads for cleaning up surfaces and bores for heater hoses and elbows
antifreeze (I only needed one gallon,)

TOOLS NEEDED:
(aside from a good socket set with extensions and universals, and a wrench set)
Thread tap 5/16-18 to clean up holes in the heads for LIM screws (only non-metric fastener I came across, the LIM screws have 3/8" heads-go figure)
10mm deep socket (for torquing two corner upper manifold screws
Inch-lb torque wrench (borrow this, or new for about $85)
O-ring remover tool (kinda like a dental pick)
Grabber tool for retrieving stuff you drop. Comes in handy for retrieving bits of broken off heater elbows and o-rings.
Digital camera to take a lot of pics of the top of the engine, so you can remember exactly how everything goes back together.

THINGS THAT YOU MIGHT BREAK (i.e., things that I broke)
Old brittle plastic heater elbows WILL break at the o-ring grooves.
Pintle caps on injectors (available from diesel injector service shops and Ebay. might be able to find an injector service kit somewhere). Not available at Autozone or any similar place.
Evaporator vacuum tubing (whole assy is 24506671, $20 from the dealer) [Autozone and similar places stock limited fittings and hose sizes these days, and you have to buy packs of multiple parts. Getting the dealer part isn't that much more expensive.]
Spark plug cables (if the ends break off when you try to remove them, you needed to replace them anyways, right?)

SOME NOTES AND ADDS TO EXISTING INSTRUCTIONS: (for GT and '99 model)
I was doing a GT, not a GTP, so there were a few differences. You don't use much torque on the upper manfold bolts, certainly not 89 in-lb as with a SC. I ended up with barely more than hand tight (does someone have a torque number for this?)

On my '99, the passenger side dogbone mounting brackets are different from the video. It's actually a bracket attached to the head next to the LIM, a top bracket where the dogbone mounts, and a bracket from there to one bolt on the exhaust. To remove the plug wires the last piece has to be removed (that was bright on some engineers part). To remove the LIM, the upper piece has to be removed, and there's a bracket on the back side which supports an alternator brace which also has to be removed prior to removing the LIM.

There is a bracket from the LIM to the throttle body that is designed to be completely impossible to remove, and prevents lifting the upper manifold and throttle body off as an assembly. [I never separated the manifold from the throttle body or intake hose] You can tease the upper manifold away from it, but there is no way to access the bolt at the LIM without removing the exhaust crossover. Brilliant. For reinstall, the lower screw hole is slotted, so leave the screw a bit loose and the bracket slides in.

I was able to remove the EGR tubing from the LIM, so I could install it separately. You might get lucky and be able to do this, depending on the exhaust placement.

IMPORTANT: The cooling elbows will very likely break at the o-ring grooves. You'll need to retrieve those pieces from the alternator bracket, AND from the inside of the LIM! To retrieve the LIM pieces, you'll probably have to remove the square cover on the drivers end of the LIM, and shake them out.