Should only be two, started with four in '96 IIRC. Pipe should have only had two holes, but they may use the same pipe for modular cars and just swap the flanges out, no big deal, it should have had plugs in the openings anyway.
The autoparts store system could be wrong...It quite often is. As stated above (4) 02's started with the 4.6L engines. 302's have the (2).....If you have completed replacement of the two you are all set!
Im having touble with the car runnin like crap, I have a code reader bringing up code 17- exhaust gas oxygen sensor signal voltage indicates rich during engine run self test or rpm too low during engine run self test