Doh, OK, re-running the script after rebooting fixed it. I must not have rebooted since updating the kernel version. Now I can run jstest /dev/input/js0and see the buttons work as well as shutdown view soft power switch and see LED indicate status.
I'm not sure if this post will be useful to others, but one never knows. In any case, the process of writing it out probably helped me figure out what went wrong.
Here is another fact, I started a new image from scratch and moved exactly the same amount of roms, the system is duplicated manually in a fresh install and it takes 2.84 seconds more to load ES on the new PI3B+ running Retropie 4.4 than the PI 3B running 3.9, its akward, but true. I have an intro video wich overlays the ES loading screen and now I have to make it that time longer because Retropie 4.4. with a PI3B+ takes more time loading.
@castroe_10 Etcher is meant to verify the image as part of the writing process. However, it may be a few things. The image you downloaded may be corrupt. It happens from time to time or the card may well be the issue. I suggest redownloading the image and starting afresh. If that doesn't yield a positive result try a different SD card.
I know the last comment on this was over a year ago, but I am having issues applying these patches. Has there been any update to this process?
I am having the exact same issue as @Dhrystone from above. Second patch fails at 1 out of 1 hunk, 3rd patch at 2 out of 4 hunks. I tried repeating the whole process, and even proceeding anyway, but the patch still does not apply, and without the second (and third?) the only difference is that now emulation station is constantly scrolling.
I know this is a serious Necro, but I'd rather not lose all the progress on the thread.