Can't dismiss follower
Nevermind I figured out how to fix my own problem, it seemed all i needed to do was reset Amazing Follower Tweaks by talking to my functioning custom follower and going through the settings to reset AFT to complete default.
Kind of acted like a reboot function which thankfully automatically dismissed all followers and allowed me to recruit my custom follower back in!
Try one (or both if one doesn't work) of these in the console;
set playerfollowercount to 0
click on the follower, type
disable
. Poof. (if you want the creature to still exist tryenable
immediately after, maybe it'll fix itself)