Old post I know, but a good subject!
I went through a number of shop made jigs over the years. They worked well enough, but as I progressed and cut more mortices, I'd upgrade with building in more flexibility to my jigs.
It was a long road, but now I have a Domino and use it extensively. $$$$ ($800 at the time).
If your boards are the same width, you can make a simple jig with two 2x4's screwed to a piece of plywood to sandwich your project. The plywood can be wide enough to fully support the router.
Cut a large square hole in the plywood around the area where you want the mortise and cover it with a piece of masonite, similar in size to your plywood. Route a slot in it sized to fit your router bit and bushing, just needs to be the right length and straight. Cut some slots in this at the ends for screws to attach it to your plywood such that you can slide it side-to-side and center it on you project. Use scraps the same size to test cut and tweak the alignment. When all set, go for it!