After trans swap - engine won't start

I just finished swapping my automatic for a manual in my 99 accord. I followed the swap DIY section and everything went smoothly except for two things. First off the car tries to start but it won't turn over. I guess it cranks but won't start. The problems I've noticed are that the green key does not flash when I turn the key like it used to. I guess this is because of the immobilizer. Do I need to now get these keys programmed for the manual ecu? Next problem is when I was showing my wife the new stereo I installed she cranked the Starter while the distributor was off. I'm guessing my timing is off now and maybe not allowing a spark to be thrown? Other than that everything was pretty straight forward but I think I have an electrical bug somewhere. Any help is greatly appreciated. Thank you guys.

The distributer only goes on 1 way so I don't think that is your problem.
The ecu needs to be programmed to the key, that's your problem right there.
I think there is a DIY on how to do it somewhere.

Yea I know the distributor only goes in one way. But my wife accidentally cranked the key when the distributor was off. That's why I think my timing maybe off. I'll look for the thread on how to reprogram my key. Thanks for the advice. I didn't think I was possible to do it yourself.

Akingkhan said:

The distributer only goes on 1 way so I don't think that is your problem.
The ecu needs to be programmed to the key, that's your problem right there.
I think there is a DIY on how to do it somewhere.

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Even when I put my automatic computer back in it doesn't turn over. It cranks but won't. Any other ideas. Anyone