I agree on the sills, think they were being harsh if they aren't rusty or got holes. I had the same thing with my old vento, they were crushed badly, but they never mentioned it. They wouldn't fail it on a dented wing now would they?
You'l be very lucky if you get it through the emissions without a cat, do they test it on what a car of that age should be producing? Or do they test the emissions on the limit a 1.8t would normally have in its usual home? I know they have different limits for different cars or different age cars. I'l be lucky with my gti powered GL, cuz they don't need a cat and they only test emissions on idle