all of the g10 3 cylinder engines are the same from 89 thru 94 with the only differences being in the engine management control sets. you can remove the intake manifold with all the sensors and throttle body from the engine coming out and reinstall it on the engine going in with no problems.
the g10 engines from 95 thru 2000 will work in the older models as well but they have a crank sensor with oil pans and oil pumps made to work with the crank sensor. you can drop a newer engine in, too, as long as you use the intake manifold, throttle body, and sensor compliment that matches the wiring and ecu of the car accepting the engine swap.
mechanically, on the long block about the only physical change is the valve cover. from 92 on they used an improved vapor condensor in the valve covers that have ribs on top. the older engines used a blocky, square looking valve cover. use the newer valve cover when you can.
about the only other thing to be aware of is that the xfi models used different pistons and 2 rings (gapless compression and a 3 piece oil control ring) while the base models used 3 rings (2 gapped comprssion rings and the same 3 piece oil control ring.) i prefer the standard engine over the xfi engine. the standard engine is rated at 55 hp and the xfi is rated for 49 hp. because of the ring arrangement most of the xfi blocks have ovaled and tapered bores. that's not to say that a standard g10 block will have better bores, the engines are infamous for worn cylinder bores if they have had a service life of over around 90,000 miles.
the last 2 engines i built both had out of spec bores. on the first engine i had the bore liners pulled, replaced, and bored to oem spec for 74mm pistons. on the second engine i had a 40 thousand over bore and used 75mm pistons from a suzuki vitara engine as replacements. i'm just including this info as a way of telling you that you will have to pay attention to machining if you rebuild one. most of these engines aren't reliable if they are rebuilt with just a quick cylinder hone and new rings.
anyway, that's the deal. you can swap in any g10 engine from 1989 thru 2000 as long as you use the ecu, wiring, sensor set, and throttle body/manifold from the car that's getting the engine. the sensor set includes the distributor as they used different ignition modules. in the 94 model year there was a half year line change where the controls shifted to the newer, improved emissions type. you can tell if you have the improved emissions set by identifying the black idle control motor on the bottom/ rear of the throttle body. you can also verify it by whether it has an old oil can coil or a newer air core coil.
there has been an awful lot written about g10 engine replacement so check the dedicated mk2/ mk3 g10 section. drill down through the threads and you will find a lot of info on these cars here on teamswift.net.