Ok, let's take it step by step again (sorry Narzoo, I know you already did it). If your file is called
eq2ui_chatprompts.xml as in the OP your eq2ui_custom.xml should look just about like this (there may be other includes):
<?xml version="1.0" encoding="utf-8"?>
<Page IgnoreTab="false" ismodule="true" Name="Custom" Size="1024,768" Visible="false">
<include>eq2ui_chatprompts.xml</include>
</Page>
Both files would be in the LP_REGION_EN_US/UI /Custom folder.
The eq2.ini would be in the LP_REGION_EN_US/ folder and look like this:
cl_ui_skinname Custom
cl_ui_subdir UI/
You would start the game via the everquest2.exe in LP_REGION_EN_US. You would open the window in game via the command (capitalization does matter)
/show_window Custom.ChatPrompts
If that does not work, the reason lies probably in the mod itself.