I had Nissen 5 weeks ago. I can't really speak to all of your issues, but I can tell you my experience:
I was instructed to continue taking Omeprazole 40 mg (my pre-surgery dose) for 30 days post surgery. I just met with my surgeon, and he told me to reduce my dosage gradually. For the past 3 days, I've been on 30 mg daily, and for the first time since my surgery, I experienced nausea and a new kind of stomach pain. I believe this is a direct consequence of my acid rebound, and I fully expect it to get worse, then better, then worse as I move my dosage down again in a month.
I also continue to experience lpr; however, my surgeon wants to give it time. He believes it will slowly get better. I, however, took matters into my own hands a few days ago, and started taking an anti-mucosal agent (Allegra-D) in the mornings. It actually really helped, and it has made me realize that I was experiencing throat symptoms from both my reflux AND another cause. I have not yet diagnosed the other cause, and maybe it really is just left-over from the reflux, but in any case, for now, I feel much better during the day.
I believe that a lot of the lpr symptoms that I'm having are just because food is not going down completely yet. It feels/tastes the same as it did prior to surgery, but my guess is that pre-surgery, the vomitus was actually coming up from my stomach through my LES, and post-surgery, the material is staying at the bottom of my esophagus for as long as hours, and then traveling back up to mimic reflux and lpr.
Of course, in my case, the vomitus is not acidic, so it doesn't burn. If yours is burning, then it would suggest to me that you have acid in there, and my story may not apply to you.
I hope your symptoms improve.