I just bought a 95 Tracker and the passenger side hub twist knob is out of sync, it appears someone has serviced them but did a poor job and did not realign the arrows, who knows if something is broke.  Has anyone taken theirs apart and rebuilt them or do I just buy aftermarket ones?

I found this guy for parts, he said he would rebuild mine for $120 plus any parts needed
http://www.wabfab.org/Aisin-Manual-Hubs/View-all-products.html

Also a good video showing what it takes to rebuild

I have rebuilt my Samurai hubs twice and a set of Tracker hubs once.  Internally, they are almost exactly the same.

Here are a few links that might help:

http://www.acksfaq.com/asinhubs.htm

http://bbs.zuwharrie.com/content/topic,92767.0/topicseen.html

Generally speaking, the Asin locking hubs (in SJ410s, Samurais and Tracker/Sidekick/Vitaras) are pretty easy to clean and re-assemble.  Once cleaned up, they operate as good as new - barring severe rusting of the springs.

Common parts that "go bad" are those springs mentioned above and the tiny ball bearing stop found on the edge of the locking knob.  Sometimes, the locking gear - which acts as a mechanical "fuse" - will shatter when SEVERELY abused.

I hope that this helps!

ive serviced mine a couple times, got one set i run, one set as spares and one set in pieces for parts. very simple to rebuild if you have the diagrams.

Rebuild them yourself.  Probably all they need is taken apart, cleaned up, lightly greased and reassembled properly.  Do one at a time, that way if you forget how it goes back together, you can use the other one as a guide (assuming it  is assembled correctly).

Yep, pretty east to clean/rebuild/grease. Just keep a close eye on the little ball bearing that is used for the knob's stop. I dropped mine twice and luckily found it. The only thing I had a problem with was one of the seals ripped during disassembly. I just cut a new one out of some "make your own gasket" paper.

This may be a relevant read.
http://www.suzuki-forums.com/suzuki-sidekick-escudo-vitara-geo-tracker/42655-cleaning-hubs.html?highlight=LOCKING+HUBS