Drinking water WITH food can dilute the stomach acids- it's important also to eat the protein first so that adequate acids are produced- when you eat veg's first less acid is called for so the protein doesn't get as well digested.
However, I've not heard Dr Nugent say to wait 2 hours after eating to drink.
What he did say was to sip all day long. He is one of the top Naturopaths in the world, president emeritus of the American Naturopath Association and president of the International Association of Alternative Medicines so I've always felt confident in following his teaching and have found them to work well.

A*****ose works better taken with your food- if you're on a no carb diet the body can turn the sugars into glucose so it should at least be taken with a bit of juice but ONLY if you are on a NO carb diet... otherwise that's ok.

Dr Nugent's point was that when you drink your water all at once it passes through the stomach where as when you sip it gets to the cells since it hasn't overwhelmed the stomach.
However, your choice. good luck.
Also to aid in the facilitating the body's absorption of A*****ose Dr McDaniel recommends taking equal amounts of Lewis Lecithin.

I am so sorry for your aloneness. I too have eperienced a lot of time alone and alienated from the life I had when I was well.
I know that friendship thought cyberspace lacks in the physical realm of hugs and smiles, but I have found that my cyberfriends have kept me sane. If you would like a cyberfriend, email me.

In terms of your glyco experience. I have not heard of anything like your experiences. The glycos I use have had very good results for people with failure to thrive which often can be a malabsorption issue and as well people with MS and muscle weakness as my own from fibro have had significant improvement with the brand I use.
Anyway, take heart. There are those of us who have lived in the world of chronic illness who do understand your situation. Few who have not experienced it have the patience to learn how life can degenerate into such a lonely place.
I'd love to correspond through email if you are up to it,
blessings,
m