It doesn't make that much difference. Engine management controls improved over the years, but HP and efficiency didn't change that much. Not sure of the Wrangler numbers, but for an XJ, between '87 and 2001, the HP jumped from 177 up to a whopping 196(the biggest improvement involved the TB, intake and head, not the electronics).
Kind of confused about your post, but if you Jeep is a '95, and has a '91 motor in it, odds are it still has the '95 FI setup. If the chassis is a '91, and has a '95 block, it's probably using the '91 electronics.(Usually, when we swap the 4.0s between chassis, the simple method is to strip the accessories from the block and use the controls and sensors from the vehicle)
The injector sequence is set by the computer. The injectors themselves are identical. To swap from the early to the late system involves swapping the computer, harness and sensors.
"Never attribute to malice that which can be adequately explained by stupidity, but don't rule out malice."
My other car is also a Jeep,.. and so is the other one,.. and that one too. How many do you own before it's "a herd" ?