02 Lincoln LS V6 auto w/ man opt ONLY drives in man, auto gears don't work, why?

What is your question?

Trans operates in manual select shift mode ONLY and gets ALL gears, but on reg automatic side it gets no gears, thus I also have no reverse. Sidenote: The idle control valve and speed control sensor (cruise control) are also bad, but I don't know if the latter, in particular, has anything to do with the issue, though the former does cause occasional stalls on start up. (I changed the former with a brand new one and the issue still persists where that's concerned) Also, I have improper air flow code for the AIR (secondary air pump system) w/ lean bank 1, but I've discovered a hole in the tube assembly from the pump to diverter valve, unfortunately it appears the tube is no longer in production. This prevents me from passing emissions as well.

What makes this problem better or worse?

Nothing makes it better, that's for sure.

How long has your 2002 Lincoln LS had this problem?

About a month with of driving with trans issue, but it's been sitting since July. Emissions was reason it was sold to me in the first place.