emmisions

i have a 99 mitsubishi eclipse 70000 miles and i cant pass emisions.the car runs fine. whenever i go i get rejected beccause my inputs such as CAT, CATHEAT,EVAP, AIR, AC, 02S,0S2HEAT, AND EGR are not ready. i figured this was happening because i recently worked on my car and the battery had to be uninstalled and the pcm needs some time to read all the sensors and inprint them to its memory but this has been happening for about a month now with the system still not being ready. im wondering if this is possiblly a problem with the pcm or because my speed sensor connector is damaged(when i was switching tranny it got crushed) so possibly the pcm thinks the car is standing still and is not imprinting this to its memory. is this a possible cause of being rejected from emisiions or is it just a bad pcm. is it possible that the VSS can affect the pcm remembering the input sensors. any thoughts are appreciated