If you have a V8 already in the truck, and in the proper location, then the FJ60 4-speed will actually move the shifter slightly rearward (about 3”) toward the original FJ40 shifter location. Your stock FJ40 transmission top cover, or the FJ60 transmission top cover, are interchangeable. Use whichever gets you closest. In my V8 swap, the V8 pulled the whole driveline forward by about 4 inches. An FJ60 top cover has the shift tower rearward on the cover, compared to the FJ40’s, so I used my stock FJ40 transmission and the FJ60 top cover, and it brought the transmission shifter to within about an inch of the original location, and it fits up through the stock hole.
For the transfer case, I had to weld in a “dog leg” on the stock single-piece transmission to get it aligned with the hole, as it was still about 3” too far forward. I cut the transfer case shift stalk above all the complex linkages and welded in the necessary length of bar stock to get it in the right position.
If your FJ60 transmission is the H42 “long” with the extra housing to the rear, this could potentially push the split case to the rear far enough that you may get lucky and have everything line up!