Ok, Nick...here is what you have so far:
1. External temp sensor fault - located on front of center brace in front of radiator (the sensor you have been wiggling) - Maybe the problem...you did mess with it afterall.
2. Internal temp sensor fault - located behind the guage face panel, behind the slats next to the cigarette lighter on the dash - maybe your problem but doubtful.
3. Solar sensor fault - the black half-dome solar eye located on top of the dashboard, dead center on the dash top - again, maybe, but doubtful.
4. Air mix door fault - located deep behind the dash near the center but behind the glovebox - probably not your problem since you get heat when heat is commanded and A/C when cold is commanded
5. Heat/AC contol panel fault - ECC panel where all the switches are - Not sure yet, but I doubt it.
6. Loss of "keep alive memory" in HVAC programmer- you remember the programmer under the glovebox, behind the dash...the tubes you and I repaired come out of it. - Don't know if you have a problem here, still have more readin' to do
7. Loss of serial data - same as above..more readin' to do.
On your delay of A/C and heat...it is normal for the system to delay operation or purge itself at start-up...the delay can be up to 20 seconds, so I wouldn't worry too much about it at the moment...if I find something that points to these conditions, I'll let you know.
My gut tells me it is the external temp sensor, or more exactly, the wiring coming out of the sensor. You have said it yourself that wiggling it keeps producing changes and that is also when the display started blinking.