I have '90 with an E4OD trans. I am not going to pretend that I have any idea of what will be involved in making the change that you propose, but I do have a thought in the matter. I wonder if you could find a '90 computer and wireing harness, would that work easier for the swap.
I am pretty sure that a '88 uses a MAP sensor as does my '90. The '95 would have used the MAF system. I don't know if it is difficult to change from one system or another that it why I am suggesting tohe posiblity of using an older computer, (but one that was designed to work with and control an E4OD.)
ANother difference that I am aware of is that the '90 uses a VSS Vehicle speed sensor mounted to the speedometer cable where it inserts into the transfer case. The '95 does not; the sensor on the top of the rear diff serves dual purpose... antilock brake, and VSS.
Good luck with this project.
Please share with us what you learned by doing it.