I swear sometimes the EQEmuLauncher is more trouble than its worth. And I can't believe all the information regarding setting up P99 without the Launcher has been removed...
Here goes:
1) 
Default install of EQ: Titanium (other clients will NOT work).  Copy/pasting the EQ folder from another install works just fine here.  (For consistency, I'm going to assume you installed EQ to 
C:\Everquest so that the eqgame.exe path is 
C:\Everquest\eqgame.exe.)
2) Right-click on the 
eqgame.exe icon within your everquest folder, select 
Create Shortcut.
3) Right-click on the 
Shortcut to eqgame.exe you created in step (2).  Select 
Properties.
4) In the Properties menu that appears, edit the 
target line to say 
"C:\EverQuest\eqgame.exe" patchme.  The quotes are only needed around the destination string if it contains spaces.  Select 
Apply and then 
OK to close the properties box.
5) Open the 
C:\Everquest\eqhost.txt file in the text editor of your choice.
6) Delete whatever is in the 
eqhost.txt file and replace it with the following two lines:
[LoginServer]
Host=login.eqemulator.net:5998
7) Save and close the 
eqhost.txt file.
8) Download the latest 
eqchangesvXX.zip file from the patch notes.  As of this post, we are on v29, found  . 
http://www.project1999.org/files/P99Files30.zip  if this post is out of date, just update "29" with the current number)
9) Extract the eqchangesvXX.zip file into the 
C:\Everquest directory, overwriting any files it asks for.
10) Within the 
C:\Everquest directory, delete the following files to allow these updated zones to function properly on P99:
arena.eqg
arena_EnvironmentEmitters.txt
lavastorm.eqg
nektulos.eqg
Nektulos_EnvironmentEmitters.txt
11) Log into the server with the account you created at 
EQEmulator.org.
12) Select 
Project1999: The Ruins of Kunark from the server list. 
13) Enjoy playing on P99.