I am trying to do the same:
http://www.subsim.com/phpBB/viewtopic.php?t=51657
EUC was made for GW 1.0 so you are missing the JIRM Rec Manual and some other things the way you installed it.
There are some other small things that annoyed me, like the rudder control being a stopwatch now. That was a good solution before the GW draggable chrono was available.
I changed the menu_1024_768.ini file in the data/menu folder and used the GW dials.cfg in the data/menu/cfg folder to get the manual working and get rid of the rudder control.
PM me and give me your email. I will mail my menu_1024_768.ini file to you, so you can see if its working for you. I am not that sure since I've made some more changes in other files (deleting them for the most part) I lost track with.