Swap all sensors and the flywheel or flexplate(required for it to run). Either swap the intake manifold,TB, and injectors, or just swap injectors and adapt the TPS to work with the HO TB. If you need to pass a visual emissions check, you'll want to use the old exhaust and intake manifolds in order to retain the EGR. If you don't have to pass this kind of testing, the best option would be to adapt the TPS, use the HO intake, use the HO header, and ditch the EGR.
I have a 93 motor/trans running on the Renix computers of my 87 XJ. I adapted the TPS and ditched the EGR in order to use the better HO manifold/bigger TB. I retained the aftermarket header I had and welded up the EGR hole, which I suppose could be done with a stock header, but would probably just be added work opposed to using the 91's header.
Injectors are important to swap because I got 11mpg running with the HO fuel injectors, back up to 16 when I intalled the Renix injectors.