I had a similar issue when I started, and I believe many on this forum did as well. I brought it up with my ortho, and he said that it's normal and so long as I'm not in pain in my jaw, I shouldn't be worried. That said, your pops/cracks, if you don't normally get them, should be brought up to your doctor. My jaw always does that, so my ortho said that if there's nothing new/painful, then I'm OK. You may want to just bring it up with your doc the next time you're in, or just call the office.
As for the non-invisibility, what can I say. It's not super invisible, people will notice, and that's part of the Invisalign experience that everyone has. That said, they're totally invisible in pictures and to people who are a few feet away from me. Definitely less visible than ceramic braces. As for speaking, I got used to them after a day or so. If you're on week 3 and still having issues, you may want to bring it up to your doc (I have a written list of questions for him every time I go in).
Good luck!
Invisalign:
23/31 U (2/3 done!)
6/6 L refinements; Completed 15/15 L
Metal braces 10 years ago