I'm really sorry you are dealing with this! It is very hard to deal with a crying baby especially when you don't have help! You need to make sure you are looking after yourself as well as him. Also, when my daughter was little I realized how easy it is to shake a baby when you are at your wits end. If you get to that point, it's better to put him down in a safe spot and go take a shower. Walk away for a little bit until you can clear your head. If you need additional help go see your OB or your doctor. It's very possible you are also dealing with post-partum on top of everything else.
As for his treatment. Did the doctors try any other medications such as Zantac (H2 blocker) or Prevacid (Proton Pump inhibtor)? You are right to be concerned about the Reglan. While it can be very helpful and needs to be used in some cases where the benefits outweigh the risks, it's use needs to be very carefully considered on a case by case basis.
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