After replacing the entire ignition system, the car will not start?

Okay. So, you replaced the ignition switch and the pass lock module. What do you mean by a "bypass module" if you mean one that is supposed to bypass the pass lock system, which is likely the first problem. When the lock cylinder and pass lock assembly is changed you need to use a scan tool to program the new module and keys in. The re-learn methods won't work if more than one security item is changed. I would remove the "bypass module" then program the security system so it functions and from there we can proceed.
Without a scan tool a locksmith should be able to do the programming.