Alex was diagnosed with silent reflux when he was 5 weeks old, and has since gone onto Losec (which is a drug that neutralises stomach acid) and it's made all the difference. His symptoms were arching his back and screaming after his feeds, sometimes screaming right up until his next feed. It took one midwife visit, three GP visits and a midnight A&E trip to get it diagnosed. It was incredibly distressing for everyone involved, but the Losec has made a massive difference and he's back to his normal happy self again.
Also, before the reflux set it we got into the habit of rocking Alex to sleep, but we've since found that the best way to get him to go down is to put him in bed when he's still awake. When he cries I go in there and pat him and shhhhh him for a bit, until he calms down and then I leave him to it. I try not to pick him up unless he gets really upset. The first few days of doing that is quite hard, but after a while the baby gets better at settling himself and you get better at learning from his cries when he'll settle himself and when he needs some help.
I guess one way to find out whether he's actually in pain or if he's just wanting more cuddles with mummy is to give him some pamol and see if that helps him settle. It's pretty harmless, as I understand it, so one 'experimental' dose should be perfectly safe. Not sure how much Tom weighs, but I think Alex was about 4.2kgs at his age and his dose then was about 1.5mls of pamol.
Hope this helps, it's not fun having an unsettled baby and not knowing what's wrong