shift linkage trouble

I have searched but haven't found everything I am looking for.
This car is a 99CSVT w/ a 3.0 in it. 2nd 4th and reverse were hard to get into. I saw that the shift tower is an issue with these cars so I checked to make sure that was ok and it seems to be fine. I then looked at the shift linkages on the tranny. The orange push in plugs? both seemed to be loose and not pushed in. I pushed them in and now I can't get it into reverse unless I move the black linkage on the tranny around first.
So I guess my questions are, what is the proper setup for those orange clips, should they be pushed in?
What does the white linkage control and what does the black one do? I think I am having issues with the black one.

Hi, just put those togther after installing a new clutch myself. The orange clips should not be pushed in. You push them in to remove them from the shift cables. I am suprised they didn't come off as soon as you tried shifting the linkage. When installing new cable ends you start with the orange clips pushed in, put them over the ends of the shifter cable and release ( with a little tab ) the orange clip out and it locks onto the end of the cable.
I believe the white one controls all gears 1-4 ( maybe in conjunction with the black one? ) but I know for sure the black one shifts into 5th. I had a bushing missing from the black one on my car and could not shift into 5th. I ordered the discontinued part from a Ford dealer that happened to have one left on the shelf. They should both "snap" into place and be very firm on the metal studs on the transmission side. If the parts guys at your Ford dealer are in a good mood, they can print you a list of all the Ford dealers with the cable ends in stock. You can search the forums here and get the part numbers.

the black cable end is for the left/right movement of the shifter while the white cable end is for the forward/backward movement of the shifter. if they are not aligned properly on the cables you will have problems getting into certain gears (depending on how they are out of alignment). to adjust them, push in the orange buttons until they lock under the retaining tab, then have someone hold the shifter in the car perfectly centered while you release the orange tabs to lock onto the cables.

check to make sure that the main engine harness is not in the way of the shifter counterweight.

Thanks for all the info. The car is at my parents house so hopefully I can get over there to look at itlater in the week or this weekend.