Randy, as long as I've known you I'd bet you've changed more of these pumps than I have. And I thought maybe I've made every coolant pump mistake possible, but then again, I know better than that. Learn something, however tiny a thing, every time.

Because of this learning process over 20 years (for me) I've not done any procedure "always".

"Other than this car my procedure has always been as follows:"

I'll take each point to comment.

"1. Clean all the mating surfaces"
This is by far the most time consuming part of the job.
"2. Lightly coat the heater pipe, the heater pipe seal (sliding the seal back against the ridge), and the interior surface where the heater pipe lives with silicone sealer."
I used to do this. RTV. Switched to Sil-Glyde (silicone grease, not RTV) but still have some old pictures showing the RTV and what it looks like the next time. Have a picture of an errant strand of it lodged in the thermostat too.
"3. Put the paper gasket in place on the studs, insert the top seal in its groove, and coat the surface of the top seal with silicone sealer"
I've been back and forth about using the paper gasket dry or smeared with grease. I rationalize the grease as preventing the paper from tearing as the pump is slid upward in the slotted holes, but then decided dry was better -- just make sure the fasteners were loose enough to allow it to move without digging into the paper.
"4. Hang the water pump on the studs, push the heater pipe into the back of the pump and partially tighten the nut/bolt combination."
I really like the flanged bolts, because a nutdriver gives so much better control at getting them started. Same with the nuts. Putting the greased square o-ring on the pipe (instead of into the pump) was the very first tragic lesson I learned on these things in '99.
"5. Install the nuts on the studs and tighten the nuts enough that the pump can still move up but eliminating the front to back movement."
Yes, this is the key, I think. Just loose enough to keep from mangling the paper gasket.
"6. Use whatever I can find room for to lever up the bottom of the pump. A length of sledge hammer handle is the most common, but if the belly pan is off I have been known to use a small bottle jack and a length of 2x4."
This, I never did understand. Why would a jack or sledge hammer be necessary to squeeze a soft rubber seal. I gave up on this many years ago, using a #1 Phillips or better, a Craftsman T-27 Torx driver in one hole as a lever. Right hand on the handle of the lever and left hand on the nutdriver to start the bolts in the remaining holes.
"7. After the pump is raised enough to start the bolts I install them; tightening those and the nuts on the studs"
Yup
"8. Tighten the heater pipe bolt."
I've forgotten to do this.

http://cleanflametrap.com/wasserpumpen.html
--
Art Benstein near Baltimore

"If you can't fix it with a hammer, you have an electrical problem." -vwbusman66