That would be awesome if you find the time to test them out as you've suggested.
It won't shock me if the little JT1 comes out on top despite giving up a large percentage of cc's to the GT80. As you mentioned, the rotary valve engine has some induction advantages over the piston port and reed valve motors .... particularly with the smaller bikes ... not so much on the larger cc motors.
Are we talking faster as in acceleration, or . . . you talking about top speed?
and . . . Is the gearing comparable on both bikes?