I have hesitated to jump in on this thread for the primary reasoning that I just didn't quite feel qualified because I've never cracked open a 390 and worked on one. I've been behind he wheel of a couple in the family over the years, changed a fuel pump on the side of I5, near Redding, CA in the summer on my Dad's '72 F250 Camper Special, but never inside of one.
The rest of this subject I've been doing the exact same thing recently, had 3 failures before what I believe to be success (so far at least) with my A Code 289, all the factory accessories present, minus one: have Thermactor, A/C and Power Steering brackets present, all having to bolt up to the water pump, and then I added an NOS Idler pulley on the A/C belt to get rid of the belt vibration I always managed to get (the books call it a "slap", but my person opinion is that term doesn't quite accurately describe it). Anyway, and something I'll NEVER ATTEMPT ever again, is to do all this tear down of the engine to detail it with new paint, replacing every single gasket that could leak with cork, paper, etc., except for the intake, restoring the original factory Thermactor Equipment and putting it back on the engine finally (been probably 15 years at least since I removed it), detailing power steering pump, installing Fred Ballard's restored, date code correct Carter fuel pump, installing a C6OE-A water pump finally....and doing this without pulling the damn motor. NEVER AGAIN! The air log tubes for the thermactor were headache enough. This car is early enough to have the lock straps on the exhaust manifold bolts, to ensure good knuckle contact when your in there tightening it all up, Autolite plugs, Kevin Marti's plug wires, etc, etc.
But back to the water pump...I have a backing plate on mine, not sure of the configuration on a 390, so there are 2 paper gaskets involved. I tried Hylomar Blue gasket sealer on it the first time, screwed it up by missing a couple of gasket holes with bolts that were angled incorrectly, leaked all over my garage floor. Took it apart again (all the brackets, fan blade, clutch fan. shroud - everything) did it again with Hylomar, leaked again after all back together (3 bolts were not tight enough, as in your case - I was too afraid of over tightening past torque specs), then finally, used 2 new paper gaskets (others were ruined) and used the gray Permatex Water Pump and Themostat housing sealer they have out there now, small tubes (bought 4) but very inexpensive. And then, just like you had experienced, thought I'd replace my twisted and bent up Trans cooling lines with new ones and had leaks there too, 3 separate times (could be/should a different thread altogether from this one). So anyway, that's my experiences thus far but I "think" I'm happy with the results so far, like having everything back to stock/original, but I sure do feel your pain (still). Feel also like I could do it in the dark dead of night now too!