Reason I chose YFZ450R suspension over regular YFZ450 is because the R has a lot longer shocks and way better valving.  I had to cut off the front of the frame and bend new tubing and make new mounts.  Also had to rework the steering stem mount.  I also added YFZ450R dual piston calipers and Z400 front hubs and stainless lines.
As for the rear shock, I had to cut all the old swingarm mounts off of the frame and swing arm.  I Tig welded a new aluminum mount to the bottom of the swing-arm.
Just had the head bored.  Head was already race ported.  Also had the head decked to run race gas.
I'm having the bottom end rebuilt now.  Genius before me used RTV as a sealant between the cases.