Just going to answer your questions. Sorry if already mentioned by others.
Leave those skills off of your bars until you get a recipe that actually requires it. Until then, don't waste your cross skill slots on them, and when a recipe that requires it comes around, swap it with your least useful cross class skill.
You definitely only want to use it when you can utilize all of its stacks. Basically look at comfort zone as +14CP as that is what's returned to you after absorbing the initial CP cost. This means you should basically start your rotation with it always when performing difficult crafts, or at the very least, before you start using CP.
Two non-specialist abilities increase progress by 33%: PbP and Muscle Memory. The thing about MM is you can only use it at step 1 of a synthesis, but is 100% success rate, while PbP can be used at any point with a reduced success rate. Remember to read the tool tips. It increases remaining progress by 33%. So it is the most useful at your initial progress increase. If you use it after, there is a high chance the progress will be even less than a careful synthesis 1. I cannot tell you if it ignores elemental affinity as I've never tried.
For this, I am going to task you with something. Actually three. Pick something to craft that is currently one level above yours and right down the progress from Careful Synthesis II. Then I would like for you to do it again with the same item when you are the same level as the recipe. Then one more time when you are one level above it. Make sure you use the same equipment during these crafts. You will notice a SIGNIFICANT increase in progress when you are one level above the recipe, and this is what Ingenuity 1 and 2 are for. Basically ingenuity 1 for same level, and ingenuity 2 for recipes higher than your current level. The less progresses it takes to complete a synthesis, the more durability you can spend towards quality.
BB is your ace card. It also stands for bread n' butter. That's exactly what it is. With enough stacks of inner quite, BB can take your quality to 100% from a very low number, and even lower if you get a modifier from 'good' or 'excellent' status. Basically, you need at least steady hand 1 up and 56 CP to use both Great Strides (32CP) and BB (24CP) combo to finish your quality with enough durability to finish the synthesis. This is why it is so important to get inner quit up at the start or near start of your craft.
Sometimes the decision is made to purposely botch a synthesis. Typically this decision is made when you have valuable mats, and nothing short of an HQ craft is acceptable. Anytime you are using expendable mats, you can forego crossing reclaim. However, when the important ones come around, you will be very happy to have this. Cross this skill when that time comes, and use it when you have a streak of failures that make HQ next to impossible.
Another crafter will have to answer this for you. What I can say is Waste Not and Waste Not 2 are kind of commitment skills. Meaning that when you use them, getting good/excellent condition procs will force you to make a decision to increase quality/progress, or sacrifice it in favor of CP. This can be stressing unless you commit to using all of its stacks towards quality/progress. The reason why I don't use WN2 is because of the longer duration of this stress.
Yup!
You are correct, it is a little tricky. There are multiple ways this skill can be used, and each of them requires an abundance of CP otherwise that CP is better spent else where. I can tell you that the only time I really use it is in the middle of my GS+BB combo. If I will still have enough CP to use BB, I will use Innovation to 'fish' for a good/excellent proc. If I don't get it, at least it still has a modifier, albeit a weaker one.
It will be important to use these skills in combination when performing difficult crafts, and this is when people start seeking out rotations, but really all one really needs to know is how the skills work (read those tooltips), and using freehand crafting to determine the next best skill to use based on the current situation. This will get you the most success throughout your crafting career.
Hope this helps, and good luck out there!