Hun, your story sounds alot like ours, except we had no NW's but almost no daytime naps so it was switched around for us!
Honestly, with reflux we found it took about a week or two to see full results as well and even then the dr told us that no meds fully cure reflux, they just help. leaving your LO to CIO will only make the reflux worse, the more he cries, themore air he swallows and then it brings the belly contents back up again, causing pain... resulting in more crying and the cycle repeats.
How do you resettle him when he does wake?
The thing with refluxers is that they arent the norm when it comes to sleeping, however if you have the time (and the energy) you can still sleep train them, I did with my Caleb, however I know that if I hadve had another child running around there probably wouldnt have been the time to do so.
I also wonder with Liz why the long wind down, for some babes this can be too long and they only need say, 20 mins.
also what kind of bottle are you trying? have you attempted a few kinds?