I don't own a jointer so my process is to rip to width on the table saw then edge joint on my router table. This has worked fine in the past including on this project.
You've got problems somewhere in your jointer setup is my guess. I'm going to go with the tables/fences not being co-planer.
I'm guessing you are using a router for a jointer. If your jointer fence isn't completely straight it can cause the board not to pass straight across it.
To use a router table for jointing, requires a 2 piece fence where the front fence is off set inward from the back fence. This allows the cutter to remove material from the infeed edge and then that edge rest/registers on the rear fence. The off set should be about 1/16" or so.
In my opinion, this set up works best with shorter pieces and will not work well with pieces longer than 3 ft or so. I would use either of two methods at this point. You can mate each pair of pieces to one another by using a hand plane and checking the gap as you proceed. The question become which piece gets the planing, but trial and error will tell you that.
The other way is to use a reference straight edge to determine where to remove the material. Use chalk, carpenter's marking crayon or Crayola on the straight edge and rub it against the work to see where the marks are left. These are the high spots which need your planing.
Jointing on a regular jointer, requires a precision setup and usually a cup or hollow on the edge means your rear table is too low. All the typical jointer issues are addressed here:
Quote from the link above:
Though less likely, the same thing can occur with a long board that already has a concave shape in the surface being jointed. If the board is too long, the ends are never on the tables at the same time and the concave shape can remain or even be made worse. If possible, cut the board to a length closer to what is actually needed for the project. You can also reverse shorter boards to help take equal amounts from both ends until it is flatter on the jointer beds. Then take all remaining cuts with the grain.