Hi there fredsmama, wow it all sounds very similar to what our little DD went through when she was that age. She had 'silent reflux' and would always spill after she had bf. She took a long time to wind and would spew up some of her feed, usually a thick, smelly, curdily vomit.
We initially used Infacol and then went on to use Baby Gaviscon. I don't know if this made much of a difference but our doctor said it might have relieved some of the discomfort she was feeling after the acidic vomit had come up. My doctor also asked me what I was eating and said that cucumber and chocolate could upset DD's tummy so I stopped eating these - it was particularly hard to stop eating the chocolate!!!!!
DD used to do her usual mantra cry to go down to sleep but then sometimes she would wake and stir, 40mins later, and make noises and then go back to sleep so sometimes her usual 'required' amount of sleep was rather disrupted. I didn't really do the pat/sh as this tended to wake her up completely. I just used to sometimes sit by her bed for 20 mins when she went down and help her out with her pacifier. She didn't really know how to use it and when she turned her head to the side it would just pop out! I am not a huge fan of paci's but this might actually have helped her out, now that I look back on it, as it might have helped her to suck and dislodge some of that yucky vomit she had brought up.
In terms of the disrupted sleep I would still get her up using the 3hr EASY even if she hadn't been asleep for very long so she was still kind of in a routine. I don't know if this was the right thing to do but she is a great little sleeper and very settled.
We also raised her bassinette and mattress; we used phone books as we found pillows and blankets too high. When she was in her bassinette the mid-wife told us to raise the actual bassinette so we popped them under the legs of the bassinette but when DD moved to a cot we put the phone books under the mattress. It didn't raise it alot but we just made sure that her feet were at the bottom of the cot so she couldn't slide down under the blankets. We often used a frontpack carrier too which is great as it allows bubs to remain upright and it gives you a free pair of hands to deal with your toddler.
I was told by our mid-wife and doctors that it would start to get better when she was about 3 months old as apparently their little esophagus start to develop abit better and they are better at controlling their heads therefore everything is more upright. We used to make sure that for about 20 mins after she had feed that she was resting upright in her little bouncinette, minus the bouncing her!! so that her feed could, as we called it, 'trickle down to her toes'.
We were about to take her to the paedatrician at 3 months and then it just kind of went away pretty much over a few nights.
I was also really worried about creating bad habits but remember your little one is still just really young and still adjusting to the world so I wouldn't worry too much about creating any bad habits and yes I would also not worry too much about where bubs sleeps. I wish I had been abit more 'chilled out' about this. I figure if they are sleeping they are restful and relaxed and it doesn't matter too much at this stage where they sleep. Just tackle one thing at a time.
I hope this helps and has not been too confusing and sorry about the length of it I sure can talk!!!!!
Good luck