There are a couple of ways to go about it.
One would be keeping the 4" long couple, and using longer threaded rods as you indicated. You could rig up a "stop" of some sort to keep that battery in place without too much difficulty.
Or you could go with the 2" coupler. The trick here is to realize that you permanently glue the coupler to one of the pieces of airframe (typically the payload). This makes it a bit tricky to load the altimeter and bits into the bay, but it's not too hard. You simply mount the alt and battery to the active bulkhead, and attach your shock cord and deployment charge, and then drop the whole thing down the top of the payload tube, wriggle it around a bit until the threaded rod ends stick out the bottom of the bay, and then mount your passive bulkhead/shock attachment/charge there. Also, one the trickiest things is gluing that coupler into the payload airframe so that it is dead straight...this is because you are only gluing it in about 1/2" deep. It's very easy to glue it up cock-eyed which is obviously not a good thing. Pay close attention during this process, and make sure it's straight before the glue sets up.
I can't post any pics right now to illustrate things, but if you search around I'm sure you can find lots of good examples.
My preference is definitely to use the 2" coupler, glued into the payload airframe.
good luck with your build,
s6