just because the saddle is costum fit doesn't mean it properly fits. I've seen lots of costum fit that put pressure points on places. A horse, even one full grown, can still grow in muscles, or roundness, making the costum fit saddle not fit anymore.
I'd check for any saddle problems and eliminate that....you said teeth were fine.
What bit are you using? Coud it possibly be too harsh for his mouth....some horses are more sensitive in the mouth than others. Have you tried a hackamore, bosal, or halter?
How old is this horse? Pictures of him would help to see if his neck stands naturally errect....if it does it will be harder for him to lower his neck until he's built the proper neck muscles.
i try to niggle it down again but he just chucks it up in refusal..he is a very touchy horse and if he dosnt like something then he will let you know by throwing his head up
This to me sounds like he's sensitive about you around his mouth, which might suggest the bit. Doesn't have to be the teeth, but the bit can be causing problems.
How is your hold on the reins? Are you riding with lots of contact, contact, slight contact, or no contact? If your not doing it already try riding with no contact what-so-ever. That there would help eliminate the bit problem, but might not solve it.
Does he do it in all 3 gaits? Or one more so than the other?