One thing is for sure, migraines come when your estrogen has fallen significantly and suddenly. Such withdrawal migraines can be severe, and can last days, even weeks, last through sleep and resist painkillers. Since some T is converted to E I wouldn't be surprised if that's your issue - you're too low on both at the end of a shot cycle, perhaps.
I don't do shots but if I had this problem I would figure it's not the dose, it's the drop-off time before the next. If so it might be fixed by shorter spacing between shots.