2000 neon won't crank
 

I recently replaced the transmission in my 2000 plymout neon.....now it won't even crank over. I tested the start and ignition switch and both are working properly. I also replaced the neutral safety switch and confirmed a good ground to the starter. I believe my issue lies with the security system. I am showing power into the ignition switch (red wire) and out of the switch on crank (yellow)....however I am not recieving a crank signal at the relay or the ignition wire into the starter. I confirmed all the relays and fuses are working properly. I have power at the neutral safety switch....until I try to crank it then I lose power there to. Does anyone have any suggestion on how I can reset the security system? Or how to confirm this is the issue?