I'm a beginner, so take my suggestion with a grain of salt. (I may be misunderstanding the problem.)
You have four choices, as I see it: You can continue with what you are doing and play like it's fine. You can take them apart and see if you can improve them doing what you've already done, but do it better. You can take them apart and re-do the whole thing by paper piecing it. You can do what mbquiltnana said. If I were taking her advice, I would make a "square up' template (maybe card stock) of my desired finished size. I would remove the black log on the ones that don't meet the desired size and make it larger. Then "square it up" to the desired size.
Given the "logs' are not the same size, and the center is not centered, you probably won't notice a small difference in the black logs. Besides, it's already "wonky" with the uneven logs. As long as the centers are lined up, you probably won't notice anything else.
bkay