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Trade you a 1995 motor with newer waterpump/t-belt for a 1999 motor.
1995 has different cams, EGR, and wiring harness/sensors. If you use the wiring harness/sensors off the 95 on the 99 engine, and disable the EGR, it will be ok.
in short, yes it will. just change the sensors. and I dont think the EGR is different Nate. Least on both my 97's the EGR is the exact same as my 95. the thing that did change is the PCV valve though (least the breather).
to deal with the pcv valve all he would have to do is swap back to the 95 valve cover cause that is different... also the cam throw the 95 cam in the 99 engine... the 95 cam is bigger then the 99.. bigger is better.. and its not to big at all, all you would notice is more power... well same as your stock 95 motor