I have new ball joints for my tracker but it appears when I remove the castle nut and pull the old joints out from the spindle, that they will hit the the axle and won't get all the way out- do the hub and axle have to be removed from the spindle to get enough room to remove and replace the ball joints? 

Yes, Take your locking hub off, then the circlip off the axle and push the axle in to move the outer CV joint inward you can get them out. Cussing might help.

Thanks, I will tackle it this weekend. I'd ask what cuss words help the most but they probably wouldn't like them in the forum. I did take the hub off and instead of a regular clip, it has a ring with 4 screws going in it. 2 of them appear to be stripped, any more suggestions?

Get those off with an impact driver, the cheep kind you hit with a hammer works fine
and the words that work best are *&^$% and |removethispart|@!$#%

Wild

Thanks, I will tackle it this weekend. I'd ask what cuss words help the most but they probably wouldn't like them in the forum. I did take the hub off and instead of a regular clip, it has a ring with 4 screws going in it. 2 of them appear to be stripped, any more suggestions?

If the heads are stripped out, take a screwdriver bit, put it on the stripped out head and firmly tap on it with a hammer....that will help loosen up the screw.  Then you might be able to turn the screw out.....if not, get a left handed drill bit and it will usuallly catch and turn the screw out before you actually have to drill the screw out (drill very slow and use lots of pressure).
For removing the non-stripped out screws....use the screwdriver bit and hammer method from above.  I have did this before and you can usually turn the screws out by hand afterwards.  Generally, on these screws, if you use an impact driver it will strip the screws out, or snap the end off the bit, before it breaks the screw loose.