i've had experiences there.. twice!!! your story is exactly what happened to me!!
i suggest the stock box to pass the epa inspection.. and then put the filter back on plus a box! (thats apparently legal!)
the emissions test is very hard to fudge!! the first time i managed to get my car running very lean, and i passed after a couple of emissions tests... (i think they may have let me off!).. the second time i had to go further being a second offence.. i had my tuner sitting in the car pulling fuel outta the tune, and i had the stock exhaust.. i also went to the emissions facility about 3 times.. did about 20 runs all up before the epa were happy!
a word of advice.. find a perm solution for being under 90dbs... only on the off chance you get done again... the second time for me was very hard to pass, plus the epa took me to court.. it wasn't pleasant, and you can bet it costs a hell of alot more than just fixing the prob!
i also suggest for the emissions test, you go to the penrith facility! alot of people told me the botany peeps weren't nice.. i found the penrith guy to be very nice and friendly!
bad luck with actually stumbling across an epa setup.. most people just complain after they get defected by a cop... all they need is a dodgy mechanic to pass them.. it sux having to go through the actual exercise...