The first step you'll have to do that you have to do is switching the motor mount from your 88-91 engine over to your new engine. Three of the mounts are on the tranny, so these shouldnt have to be changed, the only one you have to switch is the one on the drivers side of the engine. To get this mount to fit properly, you'll also have to trim the bottom of the upper timing belot cover like shown in the picture below.
A couple other things that you may want to change before putting the engine in are:
- water pump
- clutch
- flywheel resurfaceing, replacing
- head gasket, intake manifold gasket, exhaust manifold gasket, valve cover gasket....etc...
- timing belt(highly recommended)
- spark plugs and wires
- crankshaft seal
- camshaft seal
- rear main seal
- 02 sensor
and whatever other things you feel mey need to be replaced.
For the clutch or flywheel, if you have an '88, you'll need to use the flywheel, pressure plate, and clutch off of an '88 as well. so the ones designed for your tranny. Although if you have an 89-91 tranny, you can use either the 89-91 flywheel, pressure plate and clutch, or you can use the never 92-95 clutch, pressure plate and flywheel, as long as all three of those parts are from the same year, you should be ok.