02 Rubicon shifting problem Help PLEASE!!

We thought we had a code 11 so we ran through the trouble shooting diagram that was posted on here for code 11. Everything checked out ok and at the end it said to replace the ECM if everything else was ok. We replaced the ECM, When my friend first showed me the Rubicon was not flashing a code. It was just flashing continuosly. The gear shift indicator, the D1 D2 ESP and hour meter just keep flashing. It seems like the hour meter and the shift indicator D1 D2 ESP, are flashing at different rates. When I go to proform the initialization, for the new ECM, I never get the shift indicator to read N. The green light comes on indicating neutral, But the Gear indicator never reads N. When I run through the initialization, ignoring the fact that N never comes up, I hear the shift motor shift, and if I put it in Reverse Manually it does not brake up, like a rev limiter. But if I turn the key off and on, and don't initialize the system, the Rubicon will not back up without acting like the Rev limiter is coming on.

In all the intialization procedures I have read, it says to make sure the N is coming on, but none of them say what to do if it does not come on. Honda Mechanic....Can you help me with this???? I have read these forums for 3 days straight now, and I don't see anything about if the N does not come on. Any help would be greatly appreciated.

Thanks