Dang it, I don't remember which side of the filer the Schrader valve is on the 7.3 filter heads - IIRC on the 6.9 heads it's actually on the lift pump side, which I realize sounds absolutely retard but I'm pretty sure that's how it is. The location of it is important because if it's on the IP side of the filter then what drains overnight will be the filter head only, well and the IP obviously, but the filter will still be dull of fuel.
Regarding the IP chamber, I have noticed that when the pump side cover is opened for fuel screw adjustment the pump does NOT actually lose its prime, even though there's tons of fuel emptying from inside. Last two times we did that on ours we had the truck sit for several hours after pump was resealed before starting it (waiting on RTV to dry on the timing gear cover), and she lit off instantly. We have a mechanical lift pump too, so it's not a case where the e-pump filled up the IP and purged the air while the glowplugs were doing their thing...
So I am not sure if emptying the pump via the return lines actually empties the high-pressure areas as well thus killing the pump's prime, actually if you think about it the fact the engine starts easy and THEN air-locks and dies suggest the high-pressure parts of the IP do in fact NOT lose prime, and instead they push whatever fuel they have left in them into the injectors right away (that's what starts the engine) till they eventually suck air in (and that's what kills the engine).
Therefore IMHO the big question would be why your e-pump doesn't purge the air out the IP while the plugs are glowing for example - how is the thing wired, is its relay automatically triggered by the FSS?