Thanks for the advice so far.
I grew up on a ranch, and we have always started our horses out bareback until they were ready for trotting/ cantering (which is why I only want to try a brief trot with him in the pad) and we have never had problems with sore backs/ unsoundness due to it. That doesn't mean it can't happen, and I am taking the concerns into consideration. It does make sense that he may feel a bit insecure trotting bareback. He is my far the clumbsiest 3 yr old I've worked with (but thats why I love him :)).
I think he may be nervous to trot with me on his back for a few reasons. The first is that he was trained to pace, and was always taught NOT to trot when someone was driving him- I know being in a saddle is different, but he may associate driving with riding? Just an opinion.
The second is that when I got him he was being reconditioned from a tendon injury and was always told to 'go slow'. It took me a bit to finally get him to trot in the round pen after him being told to take it easy for so long.
He is excellent with voice commands which is what I usually start out with, then teach them to associate leg pressure or smooching with the voice command. He got it on the walk first try, and I know he understands what I am asking as I say 'trot' when applying leg pressure and he knows the word trot very well.
When I tried him out before buying him, with a saddle, he did the same thing when asking to trot. The woman sold him as 'green broke because you could saddle him and walk him around but he had no ground work, so I started from stratch after bringing him home. I think he may have been resisting the trot when I tried him out as he was underweight and probably very tired from not getting the proper nutrition (and if your wondering why I rode him when he was underweight was because he was all tacked up when I arrived, and I didn't realize how underweight he was until all the tack was removed afterwards :))
I will have to see about borrowing a saddle to see if that helps at all, and I figured I shoul do lots of trail riding with him to help with balance (I find it has helped build balance with young horses as they are walking over uneven ground, over sticks, etc.)
He is my first 'only mine' horse and I guess I just worry and baby him a bit too much. He is a very sweet and willing boy, and I know that when he doesn't do something I ask, he has a good reason, I only have to figure out why and fix it.