That's rough!
Maybe you could trouble-shoot the amby hammock with Trish or someone else familiar with them to make it work for you better? Sounds like he likes it better in there?
When he's in the cot, is he next to you or far away? I found being close by didn't mean they woke any less frequently, but that it was quicker to resettle, so we got more sleep overall.
Have you tried pro-biotics or anything to help his gut? no family history of allergies or anything that might account for reflux/colic?

The sleeping pattern sounds very familiar to me! I can tell you that both of mine grew out of it with time - lots of time - but in the mean time I found the only thing that 'worked' was to go with it and do whatever was easiest and resulted in the most rest possible.