The '96 will plug into the '88 frame just fine.
The issue you will face is it'll run crappy off idle.
There is a difference in the timing sensor.
What you'll need to do is either swap the CDI or the rotor.
The '88 rotor goes with the '88 CDI and vice versa.
If you opt for the '96 CDI, the connector is different on the '88 harness.
To swap the rotor you need a special puller.
http://suzukisavage.com/cgi-bin/YaBB.pl?num=1280002938