pretty the frame for a 09-2014 is different than your 99, not sure if the motor bolting positions are the same , sure maxhead flow , prodrag or scott at hillside would know if the motor mounts in the casing changed.

 

Motor/tranny/ primary will bolt in.. You might have a clearance issue with the left rear swing arm bracket but you can replace with an 07 bracket if needed.

As far as wiring goes. it will be a challenge... The 14 sg uses can bus and a BCM which means that all the instruments and switches will be needed to switched to later models if you want them to work.. You might be better off finding a 06-07 harness, TSM \ECU. It will have connections closer to the 99. 03 to 05 is a little simpler but you'd need a throttle body from that era.. You can get the wiring diagrams from the HD service info website. As Dave says, carb would be much easier. I helped a friend converted a 2000 MMI to Tmax EFI delphi replacement system and it wasn't too hard.

 

I'd be leaning in the direction of a carbed set-up, also.
Did a few years ago.
Scott