*Sigh*.. allrighty.. here we go.
1) You verified timing right? Sounds to me like one of your camshafts is 180 off... but... if you say the timing is right.. we'll take your word for it.
2) Is your firing order correct? The number one plug goes to the number one terminal on the coil? Check this to the manual and let us know.
3) Don't worry about different crank sensors. As long as you're using ALL of your EJ25 components save for the shortblock you can eliminate that possibility.
4) Double check your fuel delivery. No really.. even if you've done it three times, you've changed a lot of variables in the past week or two. Take another look.
5) The stock ECU won't care about compression ratio.. at least not right now it won't. Compression ratio has nothing to do with this issue. Eliminate that possibility.
6) How's about a compression check?
7) What's your timing look like under startup? It should be at zero. What does your timing look like under idle? Verify your timing using a timing light if at all possible.
All of these things will lead you down a specific path. A motor doesn't need all that much to run. It needs fuel, air, spark, and compression. Verify these things and you only have to worry about when they're happening, not which one isn't happening.