Received an epa notice in the mail today, never been through anything like this before so whats the best way to go about this?

Chuck your air box back on will help. As for the engine numbers, VicRoads says you can replace a engine without a road worthiness certificate but the must be the same size(cc) & with the same emissions. Is the GT3540 low mount or high mount?

This depends on whether your going in for a noise test or a full PEA inspection, if you live in ballarat chances are its noise only which is ran out the back of value tyres. I would suggest if it was my car.. definitly make it look as stock as possible but Im guessing with your GT35 you have modified all your exhaust and cooler piping to fit it. Id get a muffle plate fitted inside the exhaust, which will make it run like crap (no power) but it'll be very quiet which is what you need. With any luck they wont pick you up for the RB30 bottom end. Im not sure why you registered it with the RB30 engine number.. u should of just done the conversion.

Its a full inspection unfortunately, turbo is low mounted on a standard manifold. Are there issues with running a turbo motor as an NA for the test?