I just saw a few emails come through on my inbox thought I'd chime in on John's question.

on my ftdx-3000

Menu item 037 is set to USB

I'll have to try to see if the FT-2000 setting works better. 

I know this is a really old thread, but for anyone else searching for a solution I figured I'd report my findings.

I got it to work with a little patience.  Try configuring the radio setup to use a FT-891 for the radio selection and pick the com port on your computer that matches the ftdx3000 enhanced com port.  then for the ptt choose the FT-891 as well.  Also configure the audio to match the usb audo input and output to match the yaesu ftdx3000 settings on your computer. Only issues and this is really annoying is the frequency selection is hit or miss and many time the program will tell the rig to switch from usb data to something else or the wrong frequency.  So watch carefully when you hit the select button in winmor on your favorite node to make sure it selects it.  I had to flip back and forth between two favorites a couple of times until the dial freq on winmor matched the rig.  and as long as the rig is still in usb data, go a head and connect.   Its not perfect by any stretch of the imagination, but it will work, which will hopefully help as a last ditch effort in an emergency if you don't have one of the better supported rigs on the list.  Good luck   K9KQX