Shoot, I ran all over the desert around Las Vegas in my 1967 Ford Fairlane. Yeah, the Trackers and Kicks are made on the same assembly line. Their only differences are cosmetic.
However. More Trackers have the 8-valve engine, than Sidekicks, which got the 16 valve engine starting in 92 (Trackers started getting them in 95). The 8-valve is 80 hp, while the 16 valve is 96 hp. That's 20% more power, so look for it.
Also - not ALL Trackers or Sidekicks are 4 wheel drive, so be alert!
I ran my 2-door on 31" tires, with stock gearing - it was kind of a dog though. I recommend regearing for 31's but on 29's you should be fine (stock is 27").
Understand that your speedo and odometer will read low. When the speedo says 55 MPH, you'll really be going 59, and for every 59 miles you drive, the odometer will only click off 55 miles.
I'm still running the stock clutch (for about another few days) without any problems - you should be fine (but I DID burn out the clutch on my Fairlane!)
I would put the 3" suspension lift in - it gives you lots of options for the future. Or, maybe the Calmini 2".