So this is something that just happened when trying to leave work, basically would crank but not start and has been working fine for the last month on rebuilt motor. Had to do the first start with starter fluid but after running the primaries would start working with cranking after that.
Fast forward to tonight trying to leave work, was just cranking and no starting. After maybe 10 minutes of checking spark and fuses, I hooked up my laptop(adaptronic) and looked at the status, then did an injector test. Then tried again and started up. Not 100% sure it was the reason for not starting, but is one of the main things I can think of right now.

 

Just happened this morning after letting it sit overnight also. Having adaptronic, I can play with certain things, so I tried the injector test again but no start. Then I manually triggered the secondary injectors and had some trying to start. Not sure if maybe the fuel pressure I run is too low but may bump it up as a first theory. Once it starts, it runs fine and can restart right up.

 

Remove top plugs, disable coils and crank over and see if fuel is actually coming out the trailing plug holes.

 

My guess is the crank map is not tuned. A heat soak-ed motor might also through off the crank map.
When you "tested" the injectors, they likely opened and shot extra fuel into the chamber because you still had fuel pressure in the rail, and fired up because of the extra fuel. I change the VE%'s on the crank map in increments of 5 to find out if it needs more or less fuel.

Do you have a fuel pressure gauge/sensor? Base fuel pressure for ID injectors are 43.5pounds (aka 3 bar) IIRC.
For stock I believe it is a range between 38-41PSI but check the service manual.

 

I think it is just needing to be constantly retuned with the rebuilt motor. Fuel pressure was around 32 running with stock primaries and 2000ID secondaries, it just had me confused when it only happened after sitting awhile and only just recently after it has been good for a month so far. Started playing with the starter map this morning although the not starting didn't happen this morning. Also noticed it starts up faster with the option to have secondaries firing during cranking, but may be too much fuel as I have to give some throttle to unflood it after all that fuel.

 

Why is your fuel pressure so low?

 

Didn't really feel like it needed it, plus with it being boost related it would get upwards of 60psi at 15+ lbs of boost. I may have found a setting that was changed when uploading a map a couple weeks ago so I'll just have to wait and see if it happens again.

 

Stock FP is 38.5 if I remember right. Really no reason to run less than that, especially with the 2000's wanting a base FP of 43.5.

In the past, I have had issues with injectors that I had cleaned. I've had them get stuck open, closed, work intermittently while tuning etc. So I just upgraded to new injectors because I was tired of screwing with it.