Overall, do not be surprised that your scores have gone to crap. It takes a lot of time to get the system dialed in to where you're comfortable and you have to learn new techniques to both take advantage of and minimize the disadvantages of TIR. For instance, lots of guys complain they can't hit anything when using TIR, learn to use your forward view button to cage the TIR view along the aircraft axis for gunnery and it's better than the fixed forward view everyone is used to.
Something else to consider when you troubleshoot TIR using the heads or tracking displays. Your head movements in a fight are probably going to be much larger than when you're just sitting there moving your head around watching a graph. The adrenaline starts to pump and you may be putting in a lot of "body english" in a fight that's putting you outside the tracking limits, especially if your problem is just in one area (i.e., while looking up to the right). For instance, I find that in a fight I'll lean pretty far forward, much more than when I was calibrating TIR. This makes the tracking area smaller and centering the camera more critical. As someone else mentioned try moving your camera farther away to increase the size of the tracking area.
Here's another tip. If you've done the checks for bad tracking, clutter, positioning, etc., and you still have problems try uninstalling and reinstalling your TIR software (latest version is 4.1.30 final B). When you uninstall it'll give you the option to backup your profiles, make sure you do that so you don't inadvertently lose them. That may fix some of the problems you're seeing.
Also, while it doesn't sound as if the problem is your TrackClip Pro switch over to a regular trackclip and see if that makes a difference (make sure you switch the software settings to trackclip).
If the TIR is working as it should you may still get stutter due to your connection. Call up your "Net Status" from the clipboard (right click the map and select Net Status) and look at the Host Cue Time. Normally, this looks like an even sawtooth pattern but if you're seeing square wave patterns (instead of "spikes" the pattern has flat tops) the stutter may be due to your connection so that's what you need to troubleshoot, not the TIR. Download Pingplotter and check your average ping times and packet loss. One of the frustrating things about this is that things like dropped packets and excessive ping times don't bother you much as you're just flying around but can really show up (and screw you up) when the system is tracking multiple local aircraft, just when you need TIR the most. If your connection is causing the problems you can get lots of help by posting in the Technical Support forum.
For those of you that think TIR is great except for when you're in a fight you might reconsider your approach. Try going to the TA (I'll be happy to work with you there) and start out with simple 1v1's with a less aggressive profile and really get used to the movements. After you get used to it then step up to a more aggressive profile and so on. It can be very frustrating and disorienting when you have to "think" about what you're doing with your head but with enough practice it becomes very natural just as it took time and practice to "learn" the hatswitch views. Switching back to the hatswitch during a fight is counter productive, it just becomes a crutch and slows down (or stops) the learning process. Try unmapping your hatswitch views (except the forward view position) to force yourself to rely totally on TIR. Of course, maybe some can never adjust (getting nauseous is one of the problems) but I'm pretty sure the majority just give up too quickly.