Location of factory module, 1999 4runner

if you're referring to the factory alarm???, then it's probably somewhere under the dash, but you shouldn't need to find it. The factory alarm arms with lock and disarms with unlock. In order to disarm without unlocking for remote start, you need to hook your ground-when-running output up to the vehicle's keysense wire, which is yellow/red in the ignition harness.

Thanks chris. The keysense bypass seem to work well. I have another problem I need help with. My remote start will crank the engine but wont start if the key is not in the ignition. Could it be my key has a chip embedded in it and if so is there a workaround?

According to the info I have, some '99 4Runners had Toyota's immobilizer system on them. Assuming you're just inserting(not turning on) the key into the ignition, the immobilizer is almost certainly the problem here. In order to bypass that, you need to use a module such as DEI's 555U or 555F(the 555F is preferable since it doesn't require sacrificing a vehicle key).