I just upgraded the 6.41.4 from 4.0 so I could have the Router upgrade button work again but now I have no Winbox button. Do I need to add that to the Router Board Dude directory or something?

Add Winbox to tools:

C:\Tools\winbox.exe [Device.FirstAddress] [Device.UserName] "[Device.Password]"
Save winbox.exe in C:\Tools\
or
%HOMEPATH%\Desktop\winbox.exe [Device.FirstAddress] [Device.UserName] "[Device.Password]"
Save winbox.exe on Desktop

http://wiki.mikrotik.com/wiki/Manual:The_Dude_v6/Tools