The number of the teeth should not be a concern when thinking about orthodontics. Invisalign should be able to correct your slight overbite. The question remains as to why you are missing teeth and what is the plan for after Invisalign?. If their is active periodontal disease or rampant decay that caused you to lose the back molars then these need to be addressed first. Also, for long term stability, implants, bridge work, or a removable prosthesis should be included in the final treatment plan post Invisalign.
Any toothbrush is fine to use on your veneers. However, you must be cautious when brushing at the gumline. If the bristles of your toothbrush are too hard or abrasive or if you tend to use a lot of force when brushing, you run the risk of causing gum recession which could expose the margins of your veneers and the discolored root portion of your tooth. Always try to use the softest toothbrush available to minimize the chances of causing tooth brush abrasion. A softer toothbrush will also allow you to clean a larger surface area increasing efficiency and keeping yours gums nice and tight around your veneers.
Rotations are definitely one of the toughest movements to accomplish in the mouth. Periodontal fibers that attach to the root surface tend to pull and prevent braces or Invisalign from accomplishing the goal of alignment when it concerns rotated teeth. That's not to say that this cannot be accomplished. It does take a bit more work, such as the use of attachments for added torque and with patience the teeth will rotate and align. Invisalign in particular has done numerous studies using various shapes and positions for these tooth colored attachments to achieve optimum results. Seven years ago Invisalign would have a very tough time with this type of movement. Now with all of the research done, Invisalign can accomplish this and other difficult movements as well. So yes you should be able to achieve your predicted outcome.
Their could be two things happening. If the tray does not fit so well around the edges, this could be causing some irritation to all of the soft tissue in your mouth( i.e. lips, gums, tongue ). If the first two weeks were fine, I can only guess that you have moved to your second set of trays. Perhaps your teeth have not shifted enough and that is why the tray is not fitting correctly. I suggest you see your dentist or orthodontist that is treating your case to check the fit of the trays. If the edges of the trays are too sharp then cankor sores could be developing which can be extremely painful. The edges should then be smoothed out by your doctor. The other possibility is that you're beginning to grind on the trays at night which can cause the edges of the trays to flair out and irritate the mouth. I highly doubt that it is due to an allergy, because of the fact that you were asymptomatic the first two weeks of treatment. If your dentist does not see anything wrong with the trays themselves, then their could be some form of viral disease occuring simultaneously. Then I would proceed to check with your physician.
I've been treating Invisalign patients for the the last 8 years. The reson why your overbite is getting worse is because of the crowding on the bottom teeth. In order for the crowding to be resolved the Invisalign clear appliances will slowly expand and round out the arch. When the lower teeth are moved forward into a regular arch form, this in turn will bring your upper and lower front teeth closer resulting in less of an overbite. Invisalign is painless, efficient and better periodontally for your teeth than regular braces. I believe you should go for it!