Hello Marikaguthrie, and welcome to the forum.  Congratulations on your recent adoption of Apache.  What a great name.
What you describe as head shyness with your boy could stem from many things.  The first place that I would look would be in his mouth at his teeth.  At 11 yrs. old, if he has never had his teeth floated, he could be in need of that procedure.  A possible abscess in his gum area would be worth checking out.  You could check out both of these possibilities by gently messaging these areas.  You would be looking for discomfort on his part during the message.  When you are getting close to the problem area he will let you know with a blink of his eye before reacting by pulling away.
It is good to remember that the muscling in a horse`s jaw Is huge and very strong [one of the strongest in his body], and, when injured, takes time to heal.  Horses sometimes get kicked in this area, especially if they are running in a herd setting.  Another could be in this area, would be from a trauma that was incurred when they captured Apache.  These are wild horses at that time and they are herded into a small area with nothing but steel poles around them.
Also, another possibility could be that he had an old injury there that has healed, but the memory of his pain is still locked into his thinking.  Hence the sensitivity when being haltered.  All of these areas of question would require your GENTLE TOUCH  to bring his TRUST of your touching him in or near the affected place.  Remember, horses are anticipators, so be full of care with your gentleness.

Please keep us posted on your findings with Apache and know that we wish you much success with your new horse.
Bud

Hi marijagurthrie!
Welcome to the Uni and the forum!
Your choice to adopt a mustang from the Humane Society is such a great one, you'd wish more people would do so!
There are a lot of lessons here on the Uni about Headshy horses. 
Timing is an important factor if you want to work on a remedial problem like Apache has. 
Have you tried both sides, often horses have been handled only from the near side, bad memories are with this side. Try to work from the off side first, rubbing his head where he's OK with it and then as by 'mistake' slide your hand where he's over-sensitive. Take your hand back to where he accepts it and make your 'mistake' again... This kind of desensitizing needs good timing.  Watch Monty's videos more than once, you'll get a feel for his breathing and rhythm. 
Stay safe and keep us posted!
Miriam 

Hi. Welcome. You say you're new to the Uni so does that mean you're new to Monty's methods? My point is that you don't say you've done Join ups with Apache & with him being 11 years old you have no way of knowing his history. Great advice from Bud. My advice would be more general; to study the lessons on Join up, repeatedly, with a view to educating yourself so you can build a fantastic relationship with Apache. It doesn't matter whether or not Apache has experienced Monty's methods before. They are proven to be effective with mustangs, as well as all other equines. Study requires time & effort & I fully understand that you want to spend as much time as you can with Apache. However, my experience, with my 4 ponies, is that the time & effort is sooo worth it. Last year my 2 year old filly was lying down, completely unrestrained, in the field. She allowed me to approach, scratch her ribs with my heel ( so my leg was over her back ) & then fully straddle her body. She remained totally calm, with her ears pricked throughout & allowed me to take pictures on my phone of each stage. I had the pleasure of sharing these with Monty in person on his UK tour. All that trust was boosted because she had seen her brother & father doing the same thing, completely calmly so in her mind it was absolutely acceptable.  I'm not suggesting this is necessarily a goal for you & Apache, or anyone else. It is an example of how completely a bond can be forged, not with just 1 as yet unstarted under saddle pony but 3! Remember, the 2nd most important thing is that you have fun & the most important thing is that Apache has fun. Keep us posted with your progress. All the best. Cheers, Jo.

Thank you everyone for the comments.

Just to address some of the helpful advise brought up here. 

I don't believe that his head shyness has to do with dental issues. All the horses that go through Harmony Equine Center receive full vet care and are totally up to date on dental work before they are adopted out. It's one of the reasons I went through the rescue.

I am familiar with Monty's work and while I have not had the pleasure of attending a clinic I have watched the Join up videos extensively and have used those methods on my TWH with great results. I have been working on this with Apache. I am in a bit of a tough situation as the ranch I currently board at has no round pen or arena. So in the pasture I have been working on a form of join up since Apache of course wants to be with the rest of the herd. I can send him away and work with him as I circle the small herd of other horses. The first couple days it took me an hour to catch him. The third day it took 10 minutes. Each day seems less and less. 

I have been taking it slow with his head and stroking and petting his tense spot briefly. It seems to be working so far. But I understand it takes time. 

He is fully broke to ride, but I want to take it slow so we can build trust. I found out through his previous rescue situation that he was a wild caught mustang who wasn't gelded till he was 6. So while I think I have a great horse on my hand I think I also have a challenge.

Thanks again for all the advice!!