I just picked up an 02 Tracker 4 door. It has the 2.5 with an auto. I also have a pair of 95 trackers with the 1.6l and manual transmission. Will one of these manuals bolt up to the 2.5l?

I don't believe  they will and the ecm wont like the manual tranny. you would have to swap out pedals from a manual, clutch slave cylinder

Yep, totally different manual transmissions were put behind the 2.5 V6.  From what I can tell, the GV manual is a variation of the one that was also available in Toyota trucks; likely a variation on the Aisin built Toyota R151.

According to this link the GV had a Aisin AW5 or the AG5
May 1999– AW5 — 5-speed
Toyota Hilux, Toyota Tacoma, Suzuki Grand Vitara/Escudo

AG5 — 5-speed longitudinal
Toyota Hilux, Toyota Hiace, Suzuki Grand Vitara/Escudo, Chevrolet Niva

https://en.wikipedia.org/wiki/List_of_Aisin_transmissions#Longitudinal_rear-wheel_drive_.28transaxle.29

Don't be too quick to quote Wikipedia...

As far as I'm aware, the AW5 is a five speed automatic transmission, and in 1999, the automatics used on the GV were the four speed, 03-72LE or AW4.

The R150 (Toy), AR5 (GM), AX15 (Jeep) are basically the same transmissions, with slight variations.  Gears and bearings are the same, some differences in syncros, and differences in input and output shafts (which are interchangeable).  Changing output shafts would allow use of Toy Transfer Cases on all of them.  The Vitara's and Tracker's use a different transmission, I haven't seen a GV transmission, so I do not know.  I believe the R151 is very similar, but has different gears, requiring multiple changes to get them to work inside the others. (It has been a while since researching and playing mix & match.)
The AW5 (automatic) will not interchange parts with the listed manual transmissions.

The GV Transmission looks at like the Toyota R151.  The housing has a cast steel center piece just like the Toyota R151, and not an all aluminum housing like the Tracker/Sidekick transmission.

A couple of years ago when I changed out my GV's clutch I noted that there were several unused drilled and tapped mounting holes on the transmission.  I assumed that was due to the transmission being used in other vehicles.  The throw out bearing package also cross referenced a Toyota part number.

Toyota R151F