Modern versions of mIRC can run in portable mode, which is essentially what you have now: program files and settings all in the same folder. Thing is, I'm not sure exactly how you configure that. I know it's an option when installing.
Otherwise the settings are stored somewhere in the AppData folder in your user profile, probably under Local.
What I suggest is making sure you have a backup copy of your mIRC as it is now, installing the latest (as portable or not, depending on which way you want it to work), and then replacing the .ini files and scripts folder with the ones you have now. You'll probably NOT want to use portable mode if you're installing it in the limited-permissions Program Files folder in Windows Vista or above.
If you have trouble getting things to work, you can always keep running the old version of mIRC from the backup copy of its folder (might I suggest making a second backup, too?) until you have the new one working how you want it.