If I recall correctly, you only have a very short period of downtime between ea event, thus make sure you can get in and out of the shoes quickly. Also realize you get max points for a certain time period, but you don't get more points for doing it faster than what they deem as max.
Remember the CFA is a mathematical equation score in between these numbers you get X points, tally them, and then that is added to your WCS.
Use running as an example, you do your run in 5 min. get max points (lets say 20..I don't know the #), but you do only 1 pull up so you get 0 pts, and 45 push-ups and get 10 (assuming 20 is max), and 50 sit-ups anpther 10. Meanwhile, another cadet runs a little slower, but can do more push-up, sit-ups and pull-ups, their score can be higher than yours.
It is about the total score, don't worry so much about the shoes, concentrate more on the events. I am pretty sure since you have track shoes, you'll still run faster than the avg kid!
Finally, don't rush on taking the CFA, practice, practice, practice ---take it when you feel you can't get a higher score. DS started practicing in July and could only do 1 pull-up, and @ 50 sit ups and push-ups, by Dec, he maxed push-ups with 85, sit-ups with 90, pull-ups 13 (max is 18 for AFA). The boards aren't meeting for several months (even reg admission boards aren't until next Mar). The MOC slate can't be reviewed untill all nom files are in. In NC the noms were not submitted until Jan. You may get an LOA in August at the earliest, but LOA's are very rare, be proud if you get one, but not disappointed if you don't!
Good luck...remember practice the entire CFA under their regs, this includes the amount of downtime between ea event. Continue practicing the CFA after taking it since you want to be physically ready for USNA in July of 09