anyone know what some of the issues are doing this swap?
You should not have any issues because engines are the same
The 07 has an electric tach and single ignition signal coil and the 99 has a mechanical tach with dual signal coils. Will need some change to accomodate. Also the 07 has an oil cooler and the 99 doesn't, could be a issue with hot ambient conditions. Cooler not easily adapted to older non F model engines.
The newer bikes have a throttle sensor on the carbs. Also the ignitor box is different and some of the emissions stuff is different. Shifter has sensor for 1st and 2nd gears as well as neutral, but I've heard of people disconnecting those extra 2 wires with no problems. I think some of the extra stuff on the newer bikes deals with ignition timing and maybe timing advancement.
If you use the newer carbs with the throttle sensor, you should be OK. The basic engine is the same and the extra emissions stuff on the newer ones can be eliminated. If you go with older carbs, I suggest changing the wiring harness and use the older ignitor box.
We're going through a process of preparing a 2006 engine to go into a 1989 frame. Getting new wiring harness and ignitor for that project. Also changing the throttle to the 2 cable one from a single cable type.