What if anything needs to be changed to make a 16v out of a 96 Tracker work in a 99 16v Tracker. I know things changed in 99 but, I'm not sure on the motor. Thanks

99 has the 2.0L doesn't it?  If so it would take a lot of work to swap it out, you would probably be better off getting a JDM 2.0L or finding a 2.2 or 2.3 to drop in it.

I don't know? I just had a guy call me looking for a 1.6 16v for a 99 2 dr. Tracker. I told him I had a 96 16v motor but I wasn't sure about the ?interchangability? 

if your both of your tracker's are 5 speeds there isn't much to change.  I have an 89 tracker 5 speed, a 91 sidekick auto and a 99 tracker auto.  The 99 tracker's came with at least 2 motor sizes.  One being the 1.6l 5 speed only, 2.0l auto or stick and a 2.5l auto or stick.  There might be the odd modification like cap and rotor versus a coil.  The rad mounts a little differently.  I will check the differences between mine and let you know tomorrow if I find anything else.

Thanks looking forward to it