If you can cut up or crush your pills, or take capsules apart and add the medication to applesauce it might help you take them.
When you start eating solids again, be sure to take tiny bites and chew, chew, chew.
Did your surgeon/GI doc keep you on your PPI meds during your recovery? Many do, and it helps with the breakthrough reflux that can occur. Your newly created wrap is swollen and misshapen, and acid can sneak by. Often people recovering from a full Nissen wrap can also experience breakthrough reflux.
Also, your esophagus is a "dumb organ", and it interprets all pain as reflux. There is naturally some pain because you've had major surgery.
If you can surrender to your recovery and follow it where it leads, you'll find your recovery to be much more managable. Struggling against what is, will make things harder to deal with.
Stick around...there are lots of members here who've had Nissen surgeries. We're happy to answer questions and share our own experiences, and support you through your recovery!