Imagine that you've got both of the workpieces to be joined butted up against one another, as if they were already jointed. There are gaps; that's why you want to joint them. Clamp them both down and clamp your straightedge on one side of the joint so your router bit is in the middle of the joint. Now make the cut from one end to the other. You'll be cutting one board with one side of the bit, the other board with the opposite side of the bit. The surfaces of both workpiece edges will now be one router bit apart from each other, and every bump in one will be matched by a trough in the other.
I was suggesting that you do essentially the same thing, but do the boards one at a time, and start out with a bit of separation between them. No point in wasting all that wood with such a heavy cut.
- Owen -
P.S. A handplane, particularly a jointer plane is a good tool for this job. I didn't suggest it earlier because you mentioned that you don't have a lot of experience with hand planes. Getting short boards to mate well with a plane is easy, but a 39 incher would be more challenging. I suggest you get some scraps and try all sorts of things. You've been given lots of different suggestions. You can analyze this to death before getting your hands dirty and you'll still be surprised by the outcome.