This is because the factory bolts have extra long thread while commonly available bolts have much short threaded portion. If the bolts were as long as stock, you would run into the problem that the nuts would bottom out where the threading stops. And with the poly bushings, having a shorter bottom portion than the OEM rubber bushings, this bottom out would be the case. Thus we do ship a slightly shorter bolt with the poly bushing kits to account for that issue. It appears you have the proper length bolts 5" and 4" that we typically supply for the 1" w/ poly kits on the FJ62.
That being said, it's not uncommon for a vehicle to use a slightly different set of bolt lengths that what we designed the kit for and have been supplying parts for (our FJ62 base model had working bolt lengths of 3.5" and 4.5". Usually pops up once every year or two that some vehicle comes along that has extra long bolts from the factory because of some change in the way the bolts pass through the floor of the body or the frame bracket or something like that. If that's the case, its not an issue to swap out bolts with something longer:
4Crawler Offroad - Custom Body Lift Kits