We replaced the upper stock triple for an aftermanrlet one on my friends 07 FJR (same set up). Obviously, the ignition switch had to go into the new upper triple.
The company supplied a guide to start a drill bit bit you could do it without.
Just drill the head of the security bolts off (thier regular grade botls and drill fairly easily with a sharp bit), and slide off the ignition switch. With the triple now off, take a vise grip to the remaining studs (usually lock tighted in) and remove.
After painting, etc, replace with SS bolts (I'd use allan heads, a little safer) with some locktite, done.
PS, put a large blanket over the gas tank/front fender, etc, maybe a shop vac while drilling the two bolts, keeps metal sharps form doing evil things..
Also, obviously have the bike on the center stand. Use a sizzor jack under the header and [I]just get the ft wheel lightly touching the ground[/I]. The triple will slide on and off easily (keeping any load off it)..
This is MUCH FASTER than un-plugging and if you have to pull off the triple again for maintainance, even faster yet...