Joel,
Seems to me you are going to throw an aweful lot of money at your engine problem without actually knowing the problem...Sure, enough money and parts later you should be fine, but for how long??? You need to know the real problem and fix that first!!!
What you described is close to how my engine acted with dirty fuel; loose RPM's, then engine quits...Engine re-starts, but soon loose engine again...May start a third time, but no RPM's...Fourth try, won't start...
Running at the dock in neutral is not a good test of anything...In neutral the engine is not loaded, so very little fuel is needed to keep it running at any RPM...
I'd start with the "dirty fuel" assumption before I started changing fuel pumps ($$$) and injectors ($$$)...You should be able to look in the electric fuel pump screen, and your fuel filters to see if you see ANY LITTLE BIT OF TRASH or GROWTH...
Fuel line routing:
1. Start at the fuel tank; remove the pickup tube and be sure the little screen at the end has been removed...Should be a straight, open tube to get fuel from the tank...
2. The fuel should come out of your tank and go to the External Filter...
3. Then to the electric fuel pump...This way the external filter clogs before the electric fuel pump does...
4. Then goes to the filter on the engine...
Originally, the electric fule pump was before the external filter; this is what must be changed...Alone with removing the screen on the pickup tube in the tank...
If your diesel sat in the tank for any length of time (several months?), and you didn't add any fuel additive to prevent groowth, my bet is you have dirty fuel...
Or, if your pickup tube still has the screen on it, it has finally decayed and is blocking flow...
After removing the pickup tube screen and re-plumbing the external pump and filter, I bought 12 feet of fuel line and hooked one end to the output of the electric fuel pump, and put the other into the fuel filler neck...Turned key on and let it circulate...After about 20 minutes, I clogged a filter...Replaced filter and circulate again...I did this over and over for approx 8 hours total...Clogged several filters, but now have clean fuel (fuel output at tank fill slowed greatly when filter was clogged...At the beginning of the process, I also added "Bio-Guard" fuel additive to eat away at the growth in the tank...
My fuel is now clean...Also use Bio-Guard at every fill-up...And if fuel sits in the tank for a long while (2-3 months), may add more bio-guard later too...I mostly race, so I don't burn much fuel...
The key is to re-plumb the electric pump and filter, AND REMOVE THE PICKUP SCREEN!!!!
I also use a 20 micro external filter (vice 10 micron)...I understand the engine filter is also 20 microns, but I'd rather stop as much as I can at the first filter; easier to change when underway...
Even after removing ALL filters and pump screen, it should only tak about 1 to 1.5 minutes to bleed the system...Any more time than that, I beleive you have a growth/clogged line problem...
have your mechanic check these things FIRST!!! Could save you big $$$ and time...
Good Luck!
Tom P.