The only difference in a 4cyl gear set and a 6 cyl set is the length of the pinion. Many companys dont even make both, they make only 4cyl sets and provide a thick shim to use when installing in a 6cyl carrier.
I dont know what to tell you on the carrier bearing....they are all pretty universal. Generally the only options yiu have when buying a master install kit is v6 or 4cyl, there are no ratio / year breaks thar I can think of, atleast in the pre tacoma mini trucks.
The only thing that pops to mind is maybe the new third you bought is for a tacoma 8.4 axle....they are slightly larger and will not fit in the older 8" housing.