I understand my client version needs to be compatible with the current project client but no matter what I do I cannot get the same client version as the project is supporting. My version is 5499L, just seems like if I patch or don't patch I can't come up with the correct version to be able to use the emulator. Is there any friendly advise out there that could help me or steer me in the right direction?

Make a backup of your installation folder before you patch.

I have a 500GB drive dedicated to backups of the client files.
I just make a folder and name it the client version (e.g. 5499L) and then copy those files into that folder, then I proceed with the patching process.
One you have a compatible client, just make a shortcut on your desktop to the EverQuest2.exe file.

Hard drives are cheap these days, so don't give me the "I don't have room" bit

I have plenty of room I also have a 500 gig HD and I will give that a shot thanks for the help.

You can also use tools like SychronizeIT! to compare a "live" client with a "emu" client, and only backup the files that change, saving you considerable HDD space. But I do the same as Zco anyway, and maintain a ROK box, TSO box, Emu and Live clients simultaneously.