2005 Lincoln Aviator engine died while driving, cranks but won't start - help!

2005 Lincoln Aviator 4.6L V8 - Any advice / experience is greatly appreciated!!

Last week I was driving my finance's 2005 Lincoln Aviator when the engine
shut off while doing about 45mph. Even though the engine cut off, all
electronics and displays remained functional and bright. Moments before it
died the battery light came on which indicated to me there was an issue with
the charging system. That is the only warning I received before it suddenly cut
off.

Typically with cars I've had in the past when an alternator is failing it will start
using the battery charge until its drained resulting in dim lights, gauges, and
radio followed by the engine slowly dying but this is not what happened this
time. After the engine died I drifted into a parking lot where I put the car in
park. I turned the key off, let it still for a few seconds and tried to restart it. It
had a healthy sounding cranking attempt (battery still had plenty of juice). I
tried three more times but the car would only crank but not start.

Later that day I brought my OBD II reader to it and ran a diagnostic. The reader
said it could not run a complete diagnostic and the only code it would give me
was P1000. Upon research this code does not refer to anything specific. I also
read in her owners manual that if there is a charging system issue/battery
unplugged the car has to be driven for around 30 minutes for a complete
diagnostic to be completed (great...)

Anyways we had it towed because it was free and only a couple miles from
home. Upon return I disconnected the battery and then removed the alternator.
The alternator was tested at a local auto parts dealer and turned out to be bad.
I purchased a new one and reinstalled it with the battery disconnected. After
installation i reconnected the battery and attempted to start it. Same thing. It
cranks like normal but would not start.

Since then I replaced the following : spark plugs, coils, fuel filter, alternator,
battery, and oil/filter (it was almost time anyways). I've verified the following as
well : fuel pump is functioning and fuel rails are getting pressure, relays
(alternator, ignition, and PCM relay/"diode" checked ok) and fuses were
visually 'ok', and the battery connection is recieving a good ground. This car is
stock and has not been modified in any way shape or form (including stock
radio, speakers, etc..). After replacing the parts mentioned above the car is still
cranking but will not start. I'm in the exact same place as when i started minus
$350.

I'm a weekend garage warrior and know my way around a garage quite well
with most of my experience dealing with Nissan, Toyota (4x4's), and
Chevy/GMC. This Lincoln (Ford... arghhh...) makes me feel like I have no idea
what I'm doing and it is driving me nuts.

Does anyone have any experience in dealing with issues like this on Fords
before? My last option is having it towed to the dealership to have a diagnostic
run for around $100. I'm doing all I can to not let this Aviator get the best of
me.

Any advice is appreciated,
Nak0003