I've had a Meditor 4000Di Mk.II in my A4000 for almost a year now. I haven't experienced any jerky video using a Sapphire Radeon9250 128MB. My is loaded up with the Radeon, SB128, Ethernet and USB 2.0 and it all works good together. The higher rez screen modes are really nice. Just remember, the Radeon doesn't mode promote, so you will have to find a solution to use native mode for games and such. I use a Dell2420 monitor. The DVI is connected to the Radeon and the VGA is connected to the AMIGA video out with a C= adapter.
If you decide to get one PM me and I will send you a setup guide that will greatly help you as the one elbox provides is pretty bad.
I've got the 256MB Radeon in my A4000/Mediator setup, along with a FastATA4000, Deneb, Spider II and SB128. No graphics issues here either.
For native modes I use an Indivision. I have a Viewsonic LCD monitor and, like you, I've connected the Radeon to the DVI port and the Indivision to the VGA port. Switching displays just means pressing a button on the monitor.
I agree the installation sucks as the Multimedia CD now has updates and it isn't clear whether you should use the updates instead of what is on teh Multimedia CD or update the CD installation afterwards. Not to mention what order it should be done in. I wish they would just market a new CD with just the latest drivers and an updated installation guide.
Setting up the P96 modes is pretty straight forward once you get to grips with the P96 software. Just remember to test the modes before you save them.