Replaced ecm w/ rebuilt,car has 2 different keys, car runs security problems on 2005 Scion xB

replaced the ecm, w/ a rebuilt,co. said it wouldn't need reprogramming, just relearn,it runs, but the key for the door is different than ignition key, and it apparently has set off some security so that stereo won't work and lights are on, is there a way to reprogram the security w/o going to the dealer? found a site for reprogramming the ecm, and another for reprogramming the ignition key, but nothing on the door key.

Asked by for the 2005 Scion xB
the equipment for the programming is about 2500-3000. it is cheaper to have it done by a shop.

Thanks, for the info, any idea what it should cost to be done?