The engines are NOT interchangeable. The angle of the cylinders was changed in 1989.
If you only need a tranny then anything from the 85 and up FZ750 will work - it has always been "the trick" to drop a 750 gearbox into the 1000- why? Cause now you have a 6 speed!!! Pretty much any part in the bottom end/cases are the same.
Use http://fiche.ronayers.com/Index.cfm/Module/WhereUsed to see what parts are interchangeablw- works with any part number- just type in the number and click SUBMIT and it will tell you what all years/bikes the part goes with- works great to get a choice bit off eBay when you're not sure- of course you can use the same sight to find the part numbers if you don't have them.
Good luck
