Temmie, I would think that out of a rather modest entry level body and an "L" grade prime lens with lighter glassware than the 300/2.8 it is more than likely that the body is holding you back more than the glass. Having used neither one I am unable to be sure, but it seems a strong bet to me. By the way, when Canon was describing the focus improvements in the 40D over the 30D in the 40D White Paper they picked the 300/2.8 as their lens of choice for their example, which, if I may quote, said....
Compared to the EOS 30D, the EOS 40D’s focusing calculation speed is 1.3 times faster, and the AF data-processing time is shorter. Predictive AF can track a subject approaching at 50 kph/31 mph up to about 26.2 ft./8m away with an EF 300mm f/2.8L IS USM lens.
Now, they chose to cite the f/2.8 version, but I imagine the f/4 is no slouch either. In fact, the f/4 lens may possibly be able to focus faster, due to lighter glassware, (immesnsely specualtive there) but the f/4 aperture means the camera has less solid data to work with than with the f/2.8 lens, and thus in practice the f/2.8 lens turns in finer results.
If we look at the comments made in DP Reviews review of the 400D, regarding the 400D's AF system, they said....
Nine-point Auto Focus sensor
One criticism of the EOS 300D/350D was auto-focus, Canon has decided to bite the bullet and simply installed the considerably better nine point AF sensor from the EOS 30D in the EOS 400D. This affords both faster, more accurate focusing as well as center point AF which is compatible with F2.8 lenses.
So from thse two quotes one can easily infer that the 40D has an AF system 1.3X faster than the 400D and with superior AF performance at the outer focus points with lenses of f/5.6 and faster.
However, I have recently come to learn just how critical it is to track a moving target accurately when attempting BIF with my 50D and it is simply not good enough to wave the camera close to the subject. I look at some of your images and see that you have cropped them, so it is impossible to tell the original composition or where your focus point(s?) might be. When shooting with a shallow DOF I imagine it makes a significant difference to the results depending on whereabouts on the rider you have your focus point. It is also worth noting that, even with the 1D3, Canon's advice is to track your subject for around one second to let the AI Servogets its predictive focusing homed in accurately. I imagine a Rebel would benefit from at least as long. Apart from accuracy of aim there is also the matter of what you aim at, how well lit it is and how contrasty.
Before spending money it may be worth trying to borrow a body from the 40D/50D or 1 series range. Alternatively, if you can practice just shooting moving vehicles maybe you can determine whether the kit does have the capability but, unfortunately, you need to work on your targetting skills. e.g. if we take a look at this image....
http://appelflap.ocp-s.tudelft.nl/gallery/index.php/Wielrennen/WTOS/(2009-06-24)%20WTOS%2010km/10km2009june010.JPG
I can see the potential for quite different results depending on whether the focus point was over the hands, the upper arms, or the deep black abyss of the torso, which would have had any AF sustem completely lost, I would think.
So, my advice would be to check out your technique first of all, since without that a "better" body may not help that much, but if your technique is solid I guess you would reap benefits from a body upgrade.
EDIT : I just tried searching for "Canon's fastest focusing lens" and came across this post on POTN -
http://photography-on-the.net/forum/showpost.php?p=176616&postcount=5. It's an old post but interesting that the 300/4 is claimed to be slower to focus than the 400/5.6, yet the 300/2.8 is the fastest lens in Canon's lineup. That mixes things up a bit. Nonetheless, I suspect you should tackle the issue in this sequence....
- Check/improve technique (free);
- Upgrade body (not monstrously expensive);
- Upgrade lens (but to what, and at what cost?)