I purchased my Z in 2004 and the previous owner had an alarm installed in it when the car was new in 1995. I have since lost the remote for the alarm and wish to just replace the current system with a newer modern alarm system. I would imagine this is not to difficult considering there is already an alarm system in place. Were do I begin to look for the brain of the current system?

The "brain" is the EBCM. Here's a good write-up in hooking up aftermarket alarms:

http://www.bfranker.badz28.com/fbody/alarm.htm

I'd look into Viper, they make some good systems, good instructions and easy to hook up.