i fancy the pants of my now gym instructor it has been a while since I have seen anyone and i dont want to make assumptions.

One visit to the gym he came over when I was doing free hand weights we chatted and I arranged for him to do a new program for me, about 8 days later I had a new programme we chatted he joked and said he had just booked someone into my appointment, I must have looked disappointed for a split second then he said I was his priority. There were a couple of brushes and he shook my hand at the end.

It's a good sign that he said you were his priority and he gave you a couple of brushes and shook your hand.  It shows he is at least initially interested in you.

I saw him the following day he was a taken a back a little I had made a special effort with my hair knowing he was going to be there. We chatted again and he must have come over at least 5/6 times in 40 minutes there was some eye contact.

Again very goods signs.

I dont want things to be awkward at the gym but I have not stopped thinking about him, I am not sure how I should read the sign and if there are any or not. Is he just being a motivating instructor showing an interest I dont know? what do you think?

I think he is more than showing an interest in your fitness by the sounds of it.  With eye contact and touching, he clearly fancies something more.  But I have got to say that for both of you it sounds too early for you to be deciding whether you are interested in each other.  I think you should give it a little more time, just relax and enjoy yourself and see if he really does turn out to be the guy you want.  Don't just jump two feet into him straight away.