Thanks for the comments and suggestions guys
I'm planning on doing the luggage rack similar to the current Royal Enfield C5 frame supported rack, this will tie it directly into the frame at four points and make it strong enough for a passenger pillion seat too.
As for the rear fender even though it is a full fender and metal it is extremely light, it is a thin shaped sheet metal which won't be too heavy even with the struts and frame rails. So it will have a sub frame just on the exterior, again similar to the RE Bullets. And I think removing around 4" off the front will bring the rear tip into a much more aesthetically pleasing spot.
As for the lights tail light on the rear of the fender which I already have a cool light weight one, and possibly eliminate the turn signals entirely or possibly mount the rear signals tied in to the luggage rack or top shock mounts. I'll see once I have it sorted out and see which way will work best with not being in the passenger's way.