My 86.5 Supra seams to have a bit of trouble with water getting into the boot via the lift back. Did the Later MkIII's Have better liftback seals and can they be fitted to the 86.5?

to be honest i really wouldn't bother with changing hatches etc
generally the leaks come in 3 places...
bottom windscreen trim... it bolts on.. you will find the nuts under the boot trim in the hatch.. rip it off and re silicon it all
rear windscreen wiper... pull it out dump loads of silicon in there... wack her back in and make sure she's tight
tailights... pull em off and re silicon around the seals (if they're still there and not mushed away) or just silicon the car where the taillights bolt in... practically a squarish type shape and you should be fine after that...
other than that i can't think of anywhere else it might be leaking

good luck with the leak ;)