Ryan...
I got your pm and am answering here as this could help others in the future.
The cranking/wait/cranking/wait problem is not from the ECM/ECU. The crank (enable starter) mode is a purely electrical condition and not controlled by any microcontroller.
I would be looking at the STARTER RELAYand the MAIN relay. Look for loss of voltage at the time the "pause" is taking place. It almost sounds like the battery is weak and the relays are dropping out when the voltage drops down.
How old is the timing belt? The should be replaced EVERY 5yrs or 60k miles.. an old belt could loose teeth throwing off the timing and also damaging the valves and pistons..
They can cause the car to run (poorly) if only off by a few teeth and cause the engine to stop running completely if more than a few teeth off.
This is an "interference" type engine and a bad or broken timing belt can do a lot of damage..Look up "interference engine timing belt" on google for more info...
The TPS (throttle position sensor) or the IAC (idle air control) valve can cause flashing CELs as well as plug misfires...
You need to confirm that the fuel pump is being turned on and that there is fuel pressure on the injector rails also...
The no start condition (engine running) may be a result of cam or crank sensor problems (the ECM will NOT turn on the fuel relay and may not fire the injectors either if either signal is missing or out of time with the other sensor....
I have looked up, generated a "word" document, and posted it on my Google Drive (cloud) with the schematics for your car...Here's the link...
https://docs.google.com/file/d/0B-Yu...lZNWRlTlk/edit
Hope this helps...
Dave