I just wanted to add my 2 cents. I have a post under the bottle feeding forum re: Dysphagia/fussy feeders....you may want to read that. I posted it there (and in colic/reflux) as I bottle fed my first born. However, I bf DD (2.5 mos) and I started to notice the same symptoms with her a few weeks ago. Things only got worse as she wasn't emptying my breasts and I ended up with mastitis several times ( I produce tons of milk), so I finally admitted that the same thing was happening with DD. I had a swallow study done and hers turned out okay, but it wasn't an accurate picture as she really didn't cooperate. She screamed every time we put the bottle in her mouth and part of the study was done via syringe, which feeding from a syringe is very different from the suck/swallow activity of eating. I noticed more of a problem with bottles (which is how the study really has to be done), but she really wasn't ever a good nurser, she bobs on and off constantly and basically started to refuse my side that makes extra milk and has a fast flow. Breastfeeding is more baby-paced than bottle feeding which can make breastfeeding somewhat easier for these babies to tolerate than bottlefeeding (though that's not what it sounds like in this case-your lo screams with BF, mine only screams with the bottle).
Since the study was negative and I knew there were still issues the speech therapist and I decided to try to thicken her bottle to a nectar consistency anyway. There was some improvement, but it wasn't great. THen, reluctantly, I began to thicken to honey consistency and she's doing great. It does make breastfeeding tricky, so what I do, is BF for middle of the night feed, first thing in the morning and last thing at night. All other feeds I either give a bottle of EBM or of formula thickened. That way you can be sure that they are getting the extra calories they need during the day and aren't waking at night to feed-which will happen as they eat better sleepy, so they will want to wake to eat at night-and just because they didn't get enough cals. during the day! The pumping can become a pain, but it's worth it for the sake of your baby getting the nourishment that they need. I have weaned from one feed (by dd gets 6 feeds/day), so I BF 3x's and pump 2x's and give a bottle of formula 1x to give myself a break. I may end up weaning one more pumping session, but that's personal preference.
SOrry this is lengthy and it may not even be your issue. But, just wanted to add what I'm doing, and give details while I had some time (kids in bed). Let me know if I can help! I hope things get better!