Try here :
http://bb.bc4x4.com/showthread.php?153047-lifted-01-Vitara-2.0L-4-door-5-speed-4x4
In the 99+ models Suzuki did not offer a basic Vitara in Canada just the grand Vitara with the 2.5L v6 right?
Wrong
In order to get the 2.0L Vitara the only option is to get the tracker?
NO, tracker is the same thing anyways really.....
How do they compare?
V6's are more powerful but you pay for it in the fuel economy. The v6's are also known to have timing chain issues (tensioners), we personally have only changed a tensioner on a motor set-up we sold, otherwise our grand & xl-7 are fine. (RUN SYNTHETIC) - The 2.0L motor seems very robust.
the 2.5L is tiny for a V6 and get worst economy then the 2.0L:
correct,
Comparing numbers
2.0L has 127HP
2.5 has 155 HP
2.7 has 183HP (love it BTW) Going from an 80 HP sidekick it was culture shock
Do they both run the same transfer case and transmission?
I'm not 100% sure. Our tranny bolts up to our old sidekick t-case 
Are there any weaknesses with ether of the drive trains or between the automatic to the 5 speed?
I can tell you the automatics are great! , for wheeling, commuting, in town. Never had an issue, I have owned a Grand Vitara 2.5L Auto & my current XL7 2.7L Auto EXCELLENT trucks just crappy fuel economy.
Did they offer a tow package in ether of the newer ones?
NO problem with towing, the v6's can tow more IIRC. With our grand vitara we towed an old 16 ft trailer, NOT LIGHT tent trailer is a breeze. I'm sure the 2.0's would not have an issue.
Depending on how big your family is, I would highly recommend an XL-7 because of the 7 passenger factor & tons of room when the 3rd row is folded down. (I have 2 kids & my double stroller & lotsa groceries fit lol)
The Grand Vitara IMO is not enough for a family of 4. (it was fine we had one kid)