Factory Alarm prob

I recently bought a 98 v6 4runner that came with a factory installed checkmate alarm system with automatic start. Tha alarm seems to be malfunctioning and sometimes doesnt let me disarm. The only thing that seems to remedy this is time. Sometimes it just takes 5 min of waiting sometimes it takes hours. it just fixes itself without me doing a thing. I have replaced the remote and still hace the same prob. An alarm guy was going to charge me about way too much to check it out with no guranatees of fixing it. They said the only thing to do is to replace for about 700 bucks! Anyone ever heard of this prob.
Also I noticed that when I put on my left turn signal my headlights will turn off for a sec or two, Could these probs be related?
Sorry one more thing, How many quarts of tranny fluid does my truck take? 98 V6

Well, first off that alarm/remote start is NOT factory. 2nd, cheap alarms are very problematice around anything that transmits FM signals. Try to see if your alarm acts up in the same areas you are at.
With the turnsignal/light thing sounds like you could have a bad ground in those circuits.