Personally, I am 100% comfortable with the decision as it was made.

Here is what was found:

(2) Yamaha R1's were found to have aftermarket ram air tubes

(1) Yamaha R6 was found to have the crankcase vented to the atmosphere, where the stock configuration has it vented to the airbox. FWIW, this is not the same as the modification that Dave (MotoSix) mentioned that has been proven to be a performance enhancer.

Here are a few relevant issues:

2.2.2.C.10.d states:
Should the stock fairing include air-ducting tubes, those tubes may be removed or replaced with aftermarket air duct tubes provided they retain the stock internal area and overall shape.
Retaining "stock internal area and overall shape" is a somewhat subjective measurement of compliance.

Additionally, re-quoting what CWeed referenced (emphasis added):
Violations of technical and safety requirements judged by MRA Officials to gain a performance advantage will result in...
means that it is still up to our discretion regarding whether or not these modifications resulted in a performance advantage.

Regarding the air tubes - Are they different? Yes. But, is different always better? Not necessarily. I'll bet everything I own that Yamaha puts more R&D behind the shape and size of their ducts than Sharkskins does. Just like the kids putting a big wing on the back of a Honda Civic - it's definitely different, but not a performance advantage. In fact they are a huge disadvantage to top speed and fuel efficiency.

Regarding the crankcase breather - also not necessarily a performance gain. In the stock configuration the vent is routed to the airbox between the air filter and the throttle bodies. This area sees high vacuum under wide open throttle conditions and this actually pulls a vacuum on the crankcase. This vacuum is a performance enhancer, all the ultra-high performance engines in F1 and the like actually run a pump that is designed to run the crankcase at as much as 18" of vacuum so there is less air for the crankshaft to push out of the way. Venting the breather to the atmosphere results in a loss of this vacuum, and this could be actually be a performance disadvantage. The modification Dave (MotoSix) mentioned is something that can be done to increase the vacuum of the crankcase on GSXR's. That was not found this weekend.

Quote Originally Posted by Tumbleweed
Why would you buy $150 ram air tubes if you didn't plan on it helping.
Possibly because they are cheaper than OEM parts damaged in an accident, or to allow the OEM parts to be set aside along with the OEM bodywork to prevent them from being damaged.

In summary, while these items are violations, the board simply does not feel that the nature of the violations and the gains (if ANY) enjoyed by the riders justify a complete disqualification from the days events and loss of all points-to-date in those classes.