Brian,
Not sure how much help I can be, but I COMPLETELY rebuilt a Mercury SportJet 90 this past winter. First time ever for me and a project like this. Took my time since it was winter. All new electricals, rebuilt carbs, fuel pump, block bored 0.30 over, wiseco pistons, boysen reeds, etc.
I know mine is actually a FORCE block (junk), branded Mercury but so far at 15 hours, mine fires quickly and runs great. I pray at the end of the season this year I can still say the same thing...
Forgive me for asking stupid questions, but I'm sure you checked for even compression (didn't read the whole thread), an even spark (I have an 8 cylinder spark tester that works great) and good fuel PSI. The portable test tank sounds like a great idea, but when mine was stalling I found my fuel check valves on the fuel recirculation system were all faulty (should hear the check ball rattle when shaked). Carb rebuilds probably didn't hurt either as I found my #3 bottom cylinder carb had the wrong size jet (supposed to be larger than the other two). Also my timing was about 6 degrees advanced at WOT and I had a weak ignition coil.
To torque the flywheel nut to spec, I used a long 2X4 with 1 large 2" hole and 3 smaller holes that matched the pattern on the flywheel. I bolted the 2X4 to the flywheel (like a puller), held the 2X4 in one arm and the pulled the torque wrench with the other. WORKED GREAT!
Hope some of these ideas help. Love watching your projects!
George