I noticed one thing right off the top. In all 3 attempts, you have changed something every time. In the 2nd attempt, you changed the temperature. In the 3rd attempt, you changed the amount of meat in the cooker, you increased the cooking time, changed the rub completely, changed the temperature, and used no wood.
One of the things I figured out early on is that consistency makes good bbq. Not saying you can't change things, but change 1 thing at a time. What happens is you will end up losing the aspects you liked in favour of trying to fix the things you didn't like. Making even a simple change to a rub can change everything about the bark, the flavour, the colour. Changing the cooking time can affect all those things as well. So can changing the wood you use, or removing it completely. Adding meat to the cooker will increase the overall moisture in the cooking chamber.
For example, with pork shoulder, settle on a temperature for the recipe you're working on. Also, settle on a type of wood, and amount of wood (by weight). Then start working on your recipe. This will keep things consistent. If after a few tries, you're not liking something about it, then start making small changes. For example, if it is too smokey, look at your firing method. Then start looking at the type of wood, and the amount of wood. If it is too sweet, look at the sugar content in your rub. Too salty? Look at the salt content.
I guess what I am trying to say is if you liked how it turned out the first two times but still want to change something about it, change something small, and change only 1 thing at a time.
So to answer your questions in order:
Q1: Why no bark? (no sugar in the rub?)
A1: No sugar, no paprika, no wood (some may disagree with me on the wood part, but I feel it contributes to the bark).
Q2. Water pan only lost about half it's water on the 12hr session while most of the water was gone on the shorter cooler sessions. (makes no sense?)
A2: More meat in the pit.
Q3. Thermometer was very responsive but could it be an issue?
A3: If anything, changing temps when you're cooking could be the issue. Should also check your temps at grate level instead of just dome. My WSM dome therm is off by ~10 degrees from top grate, and 25-30 degrees from bottom grate.
Q4: Why no bark with longer and higher temps?
A4: See answer to # 1.
Q5: I'm going to poke around but is there a link to some basic tips for smoking butts on this smoker?
A5: Tons of information available here and on the Virtual Weber Bullet website.
I really hope you keep asking questions and keep trying. When you get bbq right, there is nothing like it on the planet.
Feel free to PM me any time with any questions. I should be able to help with just about anything, and if I don't know, I should know where to point you. All the best and Happy Smokin'!!!