I'm just going to list off some things off the top of my head. I'm probably forgetting some things, but yeah.
-The motor will bolt in with aftermarket mounts. Hasport makes some, not sure about other people. No idea on shift linkages but I'd assume they'll have to be changed/modified also.
-The 2000 Civic has a hydro activated clutch and the 87 Civic has a cable one. You'll either need an adapter kit or to convert the car to a hydro setup.
-2000 Civic is obd2, 1987 Civic is obd0 so you'll need an adaptor harness to run the ecu. If it were me I'd probably go obd1 off the bat and get a chipped p28 ecu because obd2 limits your tuning options down the road.
-You're lucky to have found a 87 Si because they were the only fuel injected models so the wiring will be fairly easy. Keep that in mind if you pass on this one because the non-Si models of that generation were carburated.
Red pepper racing is a very good site for the 3rd generation Civics. Here is a link to their wiki page on swaps:
Category:Engine Swaps - RPRWiki