Junior, what you are experiencing can be aggravating. It can be very frustrating chasing the perfect joint.
I pretty much gave up on the shooting board method and went back to my old Kalamazoo jointer with electric motor. Two or three passes and a near perfect joint. Not all electric jointers do a perfect job either. There was a time I went back and forth between a shooting board and the jointer, just trying to get something to work.
I hear all the folk saying planed joints are best, and that is likely true. However, I want my joints to pass the light test at the window pane and get it glued.
So many times after getting close, I'll lay two sheets of garnet paper about 180 grit on my jointer and slip the edges up under the fence. Purpose, to get that last little stubborn area of joint to flatten out and get it ready to glue. This has worked well for many many joins, and it quickly gets me past the light test.
Since I have the fence on the jointer, it serves to hold the sides or tops perpendicular to the jointer face, so no wiggling as it might doing a handheld sanding of a thin edge. I know, you may not have a jointer, so this means you'll have to devise another way to sand squarely if you choose to try it.
Some folk use an aluminum level in place of the jack plane and simply apply PSA strips (peel an stick abrasive strips) to the edge. I checked StewMac.com and they have a fret levelling tool that would work for this job it's 24 inches long and about 40 bucks.
1 Sanding on the jointer face and fence, 2 picking up from Mario to candle at a window, and 3 learning the tent method of joining have been boons to joining for me. Good luck, it's a learning process.
I still revert to the go bar deck for joining backs with backstrips so I can press everthing into alignment horizontally while joining. This can be fun once you get past the frustration of chasing the joint.
What ever works.