Congrats in the new Tracker!
I have a 2000 Tracker 2dr that started life as a soft top, but I have since installed a Rally Tops hard top.
I recently added a small lift via Old Man Emu springs. I am guessing your using a spacer lift?
There should be no reason for the rig being "squirrely" unless you did not get it aligned. I can run down the road at 70 mph all day and the truck feels very planted.
What kind of tires are you running and what size? I have 215/75R15's on mine.
Get the alignment checked.
Happy New Year.
Ps....here is mine:
upload pic