Seems the diagnostic code is triggered entirely on engine speed deceleration.
The diagnostic steps are:
1. Ignition
2. Ignition
3. Compression
4. Drive cycle
5. Drive cycle
Nothing about fuel delivery. Hm.
You've ruled out ignition, right?
And the symptoms changed when you fiddled with the injector.
I would focus on the injector.
Except you (eventually) got the same symptoms with two injectors.
The only thing that didn't change with the cylinder #1 fuel delivery is the electrical connector and the fuel rail tie. You seem fairly certain the problem is not with the electrical connection - right?
Then where do you buy your gasoline? Have you used either Top Tier gas or have you used any injector cleaners?
Because the biggest hassle of a solution here appears to be a failed ECM, and I'm having a hard time believing that's the case. After all, you are running on a replacement motor.