I would prefer to do a 6.9 over a 7.3.
-I have seen and heard of less valve a guide issues with the 6.9 and I think this is due to the valve seals the 6.9 used, which let small amounts of oil to pass by for lubrication of the guides.
-Cavitation doesn't seem to be as much of an issue with them
-As for the cracking blocks on the "A" motors, you can always delete the block heater and use a rad hose heater or something, thats what I'll have on mine for next winter.
-As for the glow plug issues, im just starting to learn the fundamentals of the 6.9 system vs the 7.3. I recently got a manual switch system working well and now time will tell if it lasts or not. Seems that most member like to switch to the 7.3 controller if they wish to keep and use a controller.
-A head stud kit seems like a popular thing to install if the heads are coming off. I like to practice head bolts re-torquing when I get an idi and then the bolts seems to hold for good. (In my experience)
-The 6.9 fuel filter header seem to be more reliable and not as leaky as the 7.3. Just have to add a better water separator or take care of the factory one.
-The 6.9 had a coolant passage left open whereas the 7.3 had the same passage blocked off for faster heating of the motor, I'd rather have it open.
-And you spoke of lower compression, well the early "A" blocks had slightly lower compression apparently. You may or may not have one. I do, rated at 155hp and its plenty peppy for me without a turbo. More so than my last 7.3 auto. What I wonder about but don't know for sure is if the lower compression is easier on the motors and head gaskets. I like to believe so.
Either way, make sure you use fuel conditioners. One thing I hate about these motors is that the injection pumps just don't seem to last. 6.9 and 7.3 used the same DB-2 pump. I usually run up to 10% bio for lubricity with good results but I won't on my current idi till I get a racor water separator on and a new return line kit. Waiting for spring