Understand this one fact - the simplest swap will be a direct replacement, and the next simplest will be swapping in an engine that the manufacturer offered as an option, which in this case are the 2.5 & 2.7 litre V6.
Move to an engine from a different manufacturer and you better either know what you're doing, or have someone who knows what they are doing perform the swap - you're going to be looking at custom everything - mounts, cooling system, fuel, intake, exhaust and a whole bunch of wiring work - in my opinion - not worth the hassle unless the vehicle is something special...
Yes - if it's a 2.0 Tracker, the brakes are going to be marginal - you can consider swapping in the brakes from the 2.5 Suzuki Grand Vitara (not the 2.5 Tracker), but you won't know if those are up to the job until you fit them & try them - I suggested it because they are larger and a simple bolt in.
In terms of suspension, how much does the 3.6 V6 weigh? If it's a cast iron V6, then yes, you'll probably need to address the suspension