The chaffing behind the neck... use Body Glide there too. No reason not to.
Putting the wetsuit on... I too used gloves so I wouldn't tear the neoprene. Although, it KILLED my knuckles to do so. So, the next time (after I knew the wetsuit was not going back)... I just cut my nails VERY SHORT (nothing hanging over the finger tip) and just pulled it up normally. Worked fine. No issues. I didn't tear anything.
Taking the wetsuit off... the key is to take it off near where you exit the water. If you notice, when you get out of the water, there is a layer of water that flows out of the wetsuit. Once that's gone, it's a struggle to get off. So, once you exit the water... step to the side and take that puppy off. It won't take that long. If you run all the way to transition and do it... it will be harder to get off.
As far as the extra material... well, honestly, the wetsuit sounds like it's a little bit too big in those areas. Not a perfect fit for your body. Just keep using the body glide on those areas. I wonder if trimming the legs would help with the behind the knee bunching?
"Life is not a journey to the grave with the intention of arriving safely in a pretty and well preserved body, but rather, to skid in broadside thoroughly used-up, totally worn out, and loudly proclaiming: WOW WHAT A RIDE!!!!"