The holes toward the front get plugged with those inserts so that you can bolt on the alternator bracket and AC/steering bracket. The holes on the back are for the thermactor system (air pump).
It will be difficult to pass the sniffer test without an air pump and cats. The air pumped to the cats is necessary for them to work correctly and if they aren't working correctly, they'll eventually get clogged.
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351W 89 Mustang GT Convertible