Hi Alkay, sure you should be able to patch up the lighter stained areas but you risk having trouble matching the stain colour. See how you go. You will obviously have to remove the tru oil on those parts. If the patch up doesn't work that well you may have to sand it all back and start again.
Up to you if you shape the headstock but to me it will personalise your build and get rid of that butt ugly square top !

Stain in the neck pocket and neck heel is only a problem for set (glued) necks, as this is a bolt on it won't make any difference.

Good luck