I would swith the accessories and bracketry over on each motor. I don't have an 88 and 95 right in front of me, but you may run into trouble trying to hook up the PS pump and AC pump. What I am saying is that the hose locations may not be in the same location on each car or you may incounter a thread pattern problem. Just something to look into first.
As for the Alternator, use the 95 Alt, it will fit the 88 bracket, if you notch it a little.
Mario
Oh also. Not sure if your 88 has mass air (Cali car or converted) but if it does I have heard that you can swap the computer from the fox into the SN95 cars. Haven't done this myself, so I am not intirely sure about this but it may be something to check out. I have heard that the computers for the 94-95 5.0 has a mild tune to it, compaired to the fox cars.