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the passenger was legally required to present the requested ID, as the US States Supreme Court has ruled that once a car is legitimately stopped the police essentially "seize" everyone in the vehicle for the duration of the stop.
once the passenger denied the request and was handcuffed is where the determination as to whether the "search" was constitutional and therefore whether the evidence is admissible. the court has also ruled, as you note, that a frisk is appropriate for their own safety. in this matter, you state "thoroughly" meaning hands in pockets??
if the officer felt something during the frisk that they felt could have been a weapon, then they could have taken the next step beyond the frisk and into the pocket.
however, it is something that a local defense lawyer should be consulted on - because there are some lines that need to be drawn - if the pat down was not directly related to the stop at hand - but instead just a suspicion that something else was taking place then the evidence being admissible is questionable. and that is what needs to be determined. even though the passenger was asked to get out of the car because he did not comply with request - was that directly related to the stop at hand or did the officer say anything that would have indicated the handcuffs and search was due to another reason.
here is a link to a very recent case Arizona v Johnson that might be of some use to you
i think i summed up everything you are now stating in my last paragraph wherein i pointed out that there are certain circumstances that would have precluded the pocket search.
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