I've just started on the EuroHolidays special missions and took out the Fokker 100 yesterday for the first time in a long while. I noticed it was sluggish in capturing altitudes and Nav course on autopilot and it also seemed to roll around at cruise as if having trouble coping with the jet stream winds...
After the flight I had a look in the aircraft file and realised why - the Fokker 100 still has the FS2002 .air file

For any of you that use this aircraft, to update it for FS2004 you'll need to copy the .air file that comes with the Fokker 100 Tay 650 variant from the Project Fokker version 2 package. (If you haven't downloaded this and are still using the Fokkers aliased to the Boeing 737 panel & sound, you're really missing out!)
Then make a backup copy of your aircraft.cfg file then replace it with the one from the "PF10070v2_F100_Tay-650" folder. Then all you have to do is replace all the [fltsim.x] sections with the one for your EuroHolidays plane (from your backup copy of the .cfg file) and you'll have a nice stable FS2004 loving Fokker to fly

I've tested it up to 4x acceleration and it captures the commanded course and FL much more accurately and no wallowing around in the wind!