I would use option 2 or 3 with an inside and outside patch. Lining up an inside dognut patch with an outside dognut can be tricky, but You can do it.
Contact adesives, like shore, are the prefered glue for hypalon, but stabond is supposed to work on hypalon as well. With stabond you can let the glue dry completly, position your inside and out side patches exactly where you want them, and then reactivate the glue with heat (a pot of boiling water placed on top works great). I have used this method several times on pvc or urethane boats, but I have never used stabond on hypalon, so you may want to confirm my understanding that stabond is compatible with hypalon. Trying to get an inside patch with tacky contact adhesive on it positioned right where you want it before it grabs can be pretty hard.
JPW has some great instructions for reactivation with heat on there website. The glue they are refering to (clifton ur 1087) is not compatible with hypalon, but it reactivates with heat in the same way as stabond.
Make sure that you put the backer nut inside the boat BEFORE you start gluing and put some wax paper in the tube under your work area to prevent the tube from gluing to itself. You can get this out throught the valve hole after your done.