You have 40 A breakers for all of the motors that need them, that is to say, the CIMs and F-Ps.
For competition purposes, it certainly isn't legal to run breakers in parallel (or series, for that matter, excepting the 20 A breaker on the compressor spike), and you have to use an equal- or lower-rated breaker for the motors.
Actually, unless it was updated/Q&A'd and not incorporated, the 2004 rule to only use CIMs and (the discontinued) drills on 40 A breakers wasn't specifically listed in the 2005 rules. Nevertheless, an inspector wouldn't likely let you get away with using a 40 A (or even a 30 A) on a little Mabuchi, Globe or a window motor, because of the low current ratings—it would allow the motor to stall and overheat, without tripping the breaker. The van door is a little trickier to judge; it stalls somewhere between 40 and 60 A, depending on the spec sheet consulted. That's too close for comfort, in my estimation, to use a 40 A.*
This rule needs to be put back in the book, for safety reasons. Unfortunately, it's easy to miss this, because all of the breakers look essentially the same, at a glance.
*A little clarification: the 60 A end of the scale should be fine, but there was a little bit of controversy early in the season as to whether or not all the van door motors were identical. Published specs for the Tiagene van door motors in previous years listed stall torque at 40 A, while the current one lists it at 59.4 A (at 12 V). If the specs are right, then a 40 could work, because it will interrupt it before stall; if a team recieved any old stock from FIRST (and some motors had strange markings on them, like "bad" stickers, and different part numbers), they might end up with a motor that will stall before the breaker is triggered. Also note that breakers don't trip instantly at their rated current; the time to trip scales with the overcurrent.