Please don't post any more unsolvable problems! How could we ever solve them??It appears that the fuel injectors are sitting properly, so i feel like it is an unsolvable issue.
When I had my injectors out I replaced all twelve O-rings and used silicone O-ring lube to help ease them back in. This is difficult as they all must go in simultaneously.
I assume you know all of the above as I assume you had to remove the injector connections when you lifted the fuel rail off.
Could it be you didn't use lube and the injectors are binding? This would prevent them from seating all the way home. And all six provide enough resistance when you're trying to do them at the same time, so you might have the impression that they were all the way on.
Let me know what you think?