To be honest, I don't understand how people play this game without a TrackIR and pedals. I just love them both soooo much.
My eyes/brain seem to have no trouble adjusting to things like TrackIR and 3D for some reason, just lucky I guess. Never had headaches/vertigo from either. IMAX has messed with me now and again though, slightly concerned if I were ever to try an HMD.
The one piece of advice I feel is worth repeating over and over and over again with TrackIR is, fiddle with the profile until you get it exactly how you like it. It is the single most personal setting you have with the game, even moreso than joystick button mappings. If you don't have it working just how you want it, whatever's bugging you will only continue to bug you. It's kind of a tedious process, but the v5 software isn't too bad to work with.
I disagree with the 'uncheck roll' crowd, but everybody's different. The important thing with the roll axis is to have it set to 1:1, so when you tilt your head, it moves the same amount ingame. I find it helps me track the orientation of my plane better for some reason.
For a single monitor setup, I think the best way to use it is with a very aggressive setup. I only need to move my head or turn my head a couple inches in any direction to get full movement. I also like to have a pretty good sized deadband in the x/y/z axes so I can get my head back to center easily for gunnery. Once my head starts moving sideways, it only takes about a couple inches to move it all the way to the side of the cockpit.
Another tidbit I didn't notice mentioned is, you can turn off TIR with F9, hit one of the hat switch buttons and let it go to put your head back to center, and then move the 'at rest' position of your head to wherever you want it with the arrow keys and pgup/pgdn, and hit f10 to save it, just like you could before trackIR. I find this very useful for getting better six views out of the F4U series for example, by moving my head as high as I can get it.
My advice would be to try other peoples' profiles and find what you like, and then tweak it to be exactly how you want it.
Wiley.