Engine won't crank after keys locked in car

My son had the keys to his 2000 Jetta locked inside his car.  We used a slim jim set to unlock the car.  When he tried to start the car after he got in, the engine would not turn over.  I've asked two vw dealerships if his key needed to be reprogrammed since he "broke" into the car.  They said that would have nothing to do with it.  I can't believe that since it was working fine before we used the slim jim to open the car.

lock and unlock car with the key

If the alarm was going off it could of burnt the battery, check to see if thats it. And it wouldn't really make sense for you breaking into your car messing up the chip in your key.

I did unlock and unlock the car manually, the remote lock/unlock is not working, however the remote will arm and disarm the alarm.
Also, the alarm did not go off when we opened the car.  I guess because the alarm was not armed.  The battery is fine.  I checked the starter and that is fine.  My next step was to check the neutral safety switch.  I took apart the console between the front seats (i read that's where you should check), but I'm not sure which wires are which.  I looked for the switch itself, but I cannot seem to find anything that looks like the part (checked parts online) inside the vehicle or in the engine compartment.  I'd hate to think i've taken the console apart and spent two days trying to find the cause if all I have to do is have it towed to the dealer and have them reprogram the key.  By the way my son only received one key when he bought the car, not even a valet key.  so, I can't even try to reprogram the key as the owner's manual described.

neutral safty switch is in the trans
you may have messed up something in the door
the plug on the door latch?

I had already taken off the door panel to look for visible damage and didn't see any.  The wires to the part that indicates the alarm is armed seemed fine and the indicator light works.  The lights flash and I hear the sound when the alarm is armed and the lights flash when disarmed.  The inside door pull cable seemed fine.  There was a rubber boot from where the door knob came out of.  I assume the door lock motor was on the other side of the boot, but I did not check for damage.   I didn't figure that would cause the problem.  Where in the door could I have messed something and how could I check.  BTW, I really appreciate the help.

the plug is on the latch you need to pull the window regulator off to get to it
it might have got pulled off by the slimjim
does your electric locks work from the switch inside the car?

No, the electric locks don't work on the inside of the car.  Actually, they quit working about 3 months ago.  I was holding the keys and must have accidently pressed something because from that point on the inside door locks quit working along with the remote door locks.  The interior light would not come on, the remote would not open the trunk, arm or disarm the alarm (exept manually).  I looked at the owner's manual and tried to reset the key.  I was only able to get it to remotely unlock the trunk and arm/disarm the alarm (remotely & manually).  The car had to be locked w/key manually.  Never had a problem starting it though.

i would check that  plug

I've tore the door apart.  I'm unable to completely take the inside panel off because it's rivoted to the door lock actuator.  Inside the door jam there's two screws that look like torx screws, however they're 12 point, which need to be removed so I can remove the acutator.  Not sure what to use to remove them (my torx set does not have one that fits exactly).  When I pull the panel away as far as possible I only see I set of wires connected to the bottom of the acuator.  I'm not really sure where the plug you speak of should be because I can't remove the latch without taking out those screws. 

I figured out that I need an 8mm triple square to remove the latch.  Does this vehicle has a starter kill as part of the alarm system? If so, how does it work, where is it, how can I test it, disable it.......
 
Thanks

that is the plug
must not be the problem