90dB isn't that hard if you have a new, stock Prius or something... Half of the new cars sitting in dealerships now wouldn't pass the current emissions or sound laws!
In all seriousness, though, just make sure it's baffled up, has adequate muffling and see how you go. I get away with my car absolutely roaring on the road - in fact it has been known to be heard over 3km away if the conditions are right...
As for the intercooler, I honestly don't see it being a problem, depending on what state you're in. You'll probably find that you'll take it to the workshop, they'll say 'nice car', tick it off and send you on your way.
Personally, I would look into fighting it - not only because the mod is probably a user certified mod, it's clearly not a case of road safety but more the result of a cop's power trip. You could always write them a letter saying you're going to the media, make a lot of noise about victimisation and you could be lucky and they'll waive it to shut you up... 
I would have got her police number and name, and made a written complaint - she's obviously gone on a power trip since you're driving a nice car. Might be something to keep in mind for the future.
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So check with the RTA, simple phone call. Then do what needs doing.