It seems like you are using more of your arm to pick than loosing your wrist to allow your hand to make the music. Is this discomfort in your picking arm or chord arm?
I have only experienced discomfort in my fingertips, thus far. It isn't on the skin level, its under the skin. It feels like the bones in the ends of my fingers are bruised. ("Played it till my fingers bled" takes on a whole new meaning. My friends told me they are bleeding under the skin)
I asked some professional guitar players (Friends of mine) Papa Duke Tinnes, Tim Allen & Gayeleen Uzzel "When do your fingers stop hurting?" The answer I got was Never. They all have decades of guitar playing experience and do play daily.
I told Coman Sproles (Another professional guitar player friend of mine) what the other 3 had said. He told me that it wasn't like that for him.
I told Dan Haines (Another professional musician friend) and he told me that it doesn't go away. Dan gave me a 20 min lesson and he did mention the shake it off method. He told me that your fingers will start to hurt after a while. Then he literally showed me how to "shake it off" and continue playing.
Each guitar player I know have callouses on the ends of their cord fingers. I am proud to say that I now have callouses on my fingers too.
It is not an EZ task to learn, can be painful, but it doesn't matter. I will suffer for my art. This is a dream of mine, to learn to play guitar, since childhood.
I put an Oscar Schmidt OSJ1 3/4 size guitar on lay away at one of my local pawn shops for $5. I had about 3 months to get it out at the price they were selling it to me for. Tim Allen, of Tim Allen's Bluestime went and bought it for me, telling me "This is a small token of our appreciation for all your hard work."
It was one of the most amazing days of my life. I owned my own guitar for the first time in my life. I now had the chance to learn to play guitar.
I will suffer for my art as long as I can manipulate my fingers to play the guitar.
(I played drums and clarinet in middle school, I can say from experience that when you stop playing an instrument, it is not like riding a bike. You do forget if you don't keep doing it)