I have a 12/74 FJ40 that I bought a top for...At the time I didn't pay too much attention when I purchased the top, only that I knew it was in good shape and had the hatch vs barn doors to match up with my lower rear swing doors.
Well, had I been paying more attention I would have noticed that despite the fact that I had rear swing doors I had a windshield frame on my 40 that had wipers on the bottom, not the top. Hmmm...The issue was that the top was setup for windshield wipers at the top (notched) of the frame. I actually had Ron at RMC install the top for me while he was doing other stuff to the 40 at the time and it worked out ok. He had to cut slots in the windshield frame channel that is attached to the fiberglass top in order to match up with the upper holes in the windshield frame that attach the channel to the frame itself.
I have since discovered that the PPO put on a '77 vintage windshield frame on my 12/74 FJ40 so thus the mismatch. Not an issue if you only run a soft top or bikini top but an issue if you run a hard top. I have pondered the thought of swapping out a correct year windshield frame channel on the top (I even actually have the channel sitting in the garage) but the concern I have is that said channel is riveted to the fiberglass top and replacing it could cause more problems than it solves.
Pick your poison but my first suggestion would be to do what Ron did and just add a couple new notches/slots to the channel where the bolt holes are on the later model windshield frame. If you don't like the results then I guess you could either find an older fiberglass top (just the top piece) with a good channel and swap them out OR do what I've been contemplating and just swap out the channels...Just keep in mind that you may ruin the fiberglass top trying to remove the old channel and install the new one. That is why I have not yet tried this and likely never will
As to the question about which wiper setup is better? I've never owned a 40 with the early style wipers at the top so I can't compare. However, I like the fact that on the later models there is only one motor (weren't their two on the earlier years?) and it is outside the cab vs. inside. The negative of the later model is that you can't buy a new motor anymore for certain years should you ever need one. I read where the later year motors were still available but that going with one of those meant you also would have to go with a later year cover. The later year cover size is different so it would be a bit of work to make it fit I'm guessing.