getting comfortable on long bike rides

As for the chafing due to the sunglasses, you might try rubbing a little Body Glide around your ears and temples (wherever the chafing is occurring). I personally don't normally have an issue with sunglasses chafing my ears, so you might want to check those sunglasses...and maybe get something else that fits better.

For the saddle sores...I haven't found the magic solution to eliminate that completely BUT you can reduce it dramatically with something like BUTT BUTTER. Which is a lanolin cream to put on prior to riding, and works really well. Sounds bad, but is a good product. Wearing good quality bike shorts that absorb moisture will help too. Finding an adequate saddle is the endless search, remember having a lot of padding is not usually the answer! More about the saddle design. Finally, bike fit is important here, if you are overweighted on the saddle, or bars, you will tend to have a sore butt, or numb hands. So check your bike fit.

As for the nutrition, didn't sound bad to me. Maybe you just had some indigestion or gas due to one or more of the things you ate. You might try eliminating something to isolate the problem, such as the nut bar or granola bar.

1. Not as familiar with sunglasses, but were you feeling anything from them before?

2. What kind of bike are you riding (road vs tri)? Sounds like road or you are sitting upright quite a bit. The glove padding does help in this case, but it takes time to build up. Are you shifting hand positions? As in turning your hands and using the various locations? Do you have an aero option to help give them a break? Also, if the pads are older or worn down they won't be quite as effective. Different types can make a noticeable difference in comfort. I haven't looked in a few years as I've been concentrating on the tri-bike.

3. Are you getting soreness or actual sores? Soreness tends to be more time in the saddle to adapt, though saddle fit is possible too. Something is really off it sores are developing. Are you standing frequently to help with his? I usually recommend every few minutes, before you have to.

4. Were you feeling anything in this area during the ride or right after? And how big of a jump was this ride? 2-3 hrs up to near 6 is pretty big. Was there a build-up to this? 6 is a big ride for anyone. I've had some funny feelings throughout the rest of the day from long rides in the past, including nausea. Some other soreness, but nothing that would be described as "horrific". It could be getting used to the duration if you're not used to going anywhere near that long. I'm doing fine in this respect on the weekly 4-5 hr rides now. Things are just tired.

2. It is a road bike, and I'm not sure what I do with my hands! I guess I move them around a little bit...but I don't think too much because at one point my hand did begin to fall asleep. Then I started readjusting and it eventually came back to me.

3. From saddle #2 it was an actual sore. Yesterday it felt like I was begin to develop one, definitely rubbing and chafing a little bit, but now that it's been a day I can see there is no sore. I'll tell you though, trying out all of these different saddles is really annoying and frustrating. I meant to add that question- will I ever find perfect comfort? Because that is what I am expecting the right saddle to have. This one I begin to feel sore and the weight on my privates from about an hour in to three hours, and then it goes away and I feel comfortable the rest. (well except having the usual tired bottom from sitting).

4. This was a real concern for me. I worked up to six hours, 10% each week. Previously I've come home with the usual fatigue and mental exhaustion where I'm just too tired to think or do anything. But I assume that is to be expected. This was something totally new. I didn't feel it until I woke up at night. I can say now that I have been awake all night I am feeling better, but not 100% yet. I did some digging around on the internet and am wondering if it was caused from not have a sports drink or electrolytes? I only drank water... and a lot of it- before, during, and after!

a cycling bib can help.

2 and 3 are likely related.  If you bottom is not happy, you will instinctively transfer weight to your hands without thinking.  That will wear on you after 6 hours on the bike.  If you aren't using some sort of chamois cream, then invest heavily.  That sort of endurance riding requires it.

With respect to 4, what pace are you riding at and what are the conditions?  6 hours is a long time on a bike for how much fluid and calories you consumed.  You are looking at a total of roughly 800-1000 calories for a 6 hour effort.  Unless you are rolling downhill, you will likely burn through far more than that during the effort.  Most of us need more than that amount for a sedentary shift at the office.  I would also look at the temperature of the day coupled with your salt intake.  You didn't take much electrolyte during the ride, so there is a good chance your electrolytes were imbalanced. 

You know what they say about electrolytes?  They are what plants crave!