Suddenly scared?

Our boy Saxon has been acting a little weird today, after spending all day with him, we went out for dinner and with friends for a bit, after we got home he greeted us at the door he became very cautious and slowly moved towards the back door like there was something out there. We turned the backyard light on and nothing was out there. We took him to our bedroom as we were getting ready for sleep and he sleeps at the foot of our bed and he was being very playful and trying to chase his tail but he had burnt his paw the last couple of days so we didn't want to engage him in play to much in case he aggravated it. I picked him up and fell gently into bed holding him (as I do with him often) and he freaked out! he jumped out of my arms and half way across the room and didn't land on his feet. when he got  up was very very wary and scared. My partner picked him up for a while and he was fine but then after 10 minutes sat in bed with him and again he freaked up and scratched her up good, he never used excessive force until then. again he was very cautious, and looking up at the bed sniffing around holding his paw up. He sniffed around alot of the room jumping any time we made a noise. eventually he went out of the bedroom and went to his area near his scratching post in the living room. We needed to go to sleep as it was after midnight and I had to get up at 6AM, he didn't come to bed which was weird for him but slept on a pile of my partners clothes else where in the house.

This morning he was less on edge but still not normal he still didn't want to come into our bedroom, away from it he was he a very loving cat and was all rubbing up against us. He was very scared off the pantry where his food is kept where normally he tries to get all up in there.

Can cat pain killers or antibiotics affect behavior? Or has something just really spooked him?

The attack on your partner sounds like redirected aggression.  Could he have seen something outside--another cat or other animal?  That can really freak out a cat, especially if he's already hurt and feeling wary. 

It was less of an attack towards my partner and more of a "I want to get out of here as quick as I can thanks" I have found other cat poop in the backyard before, our bedroom is on that side of the house. perhaps he got a visit last night when we were out?

It could very well be.  There are repellants like this  that you can use to keep other animals away from your yard.  Inside, you could try a Feliway plug in to calm your cat, or Feliway spray on your bed. 

We had a neighborhood cat coming in our cat door and terrorizing our cats.  We had to change the kind of door we had so it couldn't get in any more.  It took several weeks for our cats to stop being spooked after the strange cat stopped coming around the house, but eventually they got over it and went back to their usual sweet selves.

A couple of days have passed and his behavior is still puzzling. He was starting to get back to his old self and be super affectionate. But today again he has been very anxious did not like to be held, walked away when he was being petted. Could it be a possible side effect of the pain medication and antibiotics?

Has Saxon been ill? What are the pain meds/antibiotics for?

Last Friday he jumped up on a hot plate just a couple of minutes after it was turned off and my partner was serving up a meal. We took to the vet and got antibiotics and pain killers. He was his same old self until Sunday and he has been off ever since.

It seems to have with smells to do.  You seems to have got foreign smells into the house and possibly - on your partner.

OR alternatively, the medicines had affected his smell senses - which I think is possible, although I dont remember any proofs at this moment.   (phone this your vet and ask?)

anyway, under the time you can try and work with stressing him down.  for example, use  Feliway.  Or  dr Bach´s Rescue Remedy  (google on it).  

Relaxing music may also be helpful. classic harp music is best, but most could do.

Hmmm not sure about smell, tonight he has been more normal than he has for a while but every now and then something spooks him and he jumps up about 3 foot in the air. If we are holding him at that moment he rips you to shreds when he springs up, his claws need clipping but it looks like it could be a dangerous undertaking. He has been alot more playful tonight as well but he still is very hesitate to come in to our bedroom, which is weird as before this week he slept with up every night since we got him.

Poor little guy.  He could be wary from the accident; it could be the meds (as Stefanz say, it might be a good idea to phone your vet and ask about that); it could be another animal outside.  Calming him down would be the main goal.  I do recommend Feliway.  I have used it successfully calming down cats.  You might want to try using the spray--spray it on and around your bed where he sleeps.  Or try a calming collar.  I always tell people about these:  www.calmingcollars.com  (single wide, extra small is about cat size).  The herbal collar worked wonders for one nervous cat I had.

Oh--about the claws.  Do you have a Petco or someplace like that nearby?  If they have a groomer onsite, they will clip nails at a reasonable price.