First thing to check - is the reflux fully controlled now? No pain?
Personally speaking if she is fully well I would get her into the inclined bed and drop the swaddle all at once. To my mind there's no sense in sleep training only to have to do it all again when you change something else. But if you want to do it one at a time that's fine, you could use a more gentle weaning strategy for the swaddle in a month or two. This link is quite useful:
Weaning the swaddle - when, how, tips and tricksAs she is a refluxer I would avoid PUPD all together - it's not recommended as the PUPD action can really aggravate the condition. It's also only really to be used as a last resort for babies from four months in whom shh pat has been tried consistently with an appropriate routine without success. Shh pat can be adapted to whatever your LO prefers - if no shh and a hand on the chest is what suits her, then go with that
. Just make sure that you work on removing your hand earlier and earlier so she can do more of the falling asleep on her own.
Some babies always cry before sleep, that can just be their way of letting off steam. Sleep training may or may not change that. Can you tell the difference between an 'I need you' cry and just a frustrated, tired cry?
Nap resettling.....well I gave up on it mostly. It just stressed me out! But if you are going to do it I would set yourself a time limit e.g. 15/20 mins and if LO hasn't resettled by then just get up and move on with the day. And shorten the next A time a touch to try to minimise OT.
Her EASY looks great - well done