The ball joint stud is tapered. The spindle hole has a matching taper. You cannot pull the ball joint into the hole
farther than the taper will allow. From the photos it seems like you have the same number of threads extending
past the ball joint nut that I do. That makes me think your ball joint is fully seated. I agree it should not be that
hard to change a ball joint, but you have to remove the strut (if you don't want to ruin the alignment), then you
have to remove the control arm which even when fully extended has a tremendous amount of energy stored in
the spring. Just from a safety aspect you have to consider if this is something you want to attempt yourself. But
most importantly, is the ball joint really the culprit? I think you need to make some additional measurements. I
will compare those measurements against my own 2001.

 

I fished a tape measure over the control arm and around the ball joint on my Tracker.



The loop included the length of ball joint stem and nut.




I measured 10-1/4".

 

I investigated the "wrong control arm" theory as much as I could. These are the part numbers for my 2001 Tracker.





The RockAuto numbers matched those (in red) I found on another Tracker parts site. More importantly, all
three engine sizes, 1.6, 2.0 and 2.5, use the same control arm. There was an additional part number (in orange).




RockAuto shows the orange part number fits all Trackers from 1999 to 2004. It's hard for me to imagine a scenario where a wrong control arm would even be available.

 

I’m at a control arm on it. Guess I’m going to pull it down soon as I can and see what I can find out. It’s odd that it’s both sides. Maybe the hole that the spindle go in is to small.

 

by your picture it looks as if you can see the ball joint threads on top of the control arm. is this true? you should only be able to see the smooth part of the shaft. is there any pin or anything that holds the nut in place? i would think if the ball joint was broken it would cause more damage but a loose nut slowly backing off the ball joint would cause it to slowly start grinding the cv shaft as your is done

 

It's possible someone installed incorrect control arms. It's possible someone installed spindles with holes too small.
It's possible someone pressed incorrect ball joints into a non-repairable control arm. But none of those situations
seem likely to me. Here's how much of the ball joint stem should extend past the bottom of the spindle. Please
compare these measurements to yours. (Did you measure around the control arm/ball joint circumference?)





Something is terribly wrong if you can see threads under the rubber boot.




If you decide to remove the ball joint you will need a tool like this. Harbor Freight sell this one for around $20.
Do not attempt to remove the ball joint (or tie-rod ends) without one.

 

Looks like my measurement is 11 1/4 were toured is 10 1/4. But I have 7/8 of the ball joint sticking out of the bottom.

 

Check for play in the ball joint. This video gives an idea of what you are looking for.