#1. I had to make a list of the songs I know, so I could make sure I play them all once in a while. I’ll occasionally scan through the list and look for songs I haven’t played recently.
#2. When I go back to a song I know with plans to decorate it a little, I usually pick one measure or one phrase, and just mess around with it over and over until I find something interesting that works. A bit of trial and error. After that, I’ll play through the whole song and see how it sounds.
#3. I definitely had this same issue. I think you will just naturally work this out. As you get more and more comfortable playing (and hearing) the song, you’ll just sort of know whether you have played the A part twice or not. If you are playing the same version of the A part for both, you might want to try to learn a variation of the A part for the 2nd run through (like Ben teaches on most of his lessons, for mandolin at least). Then it’ll be a little easier to tell which A part you are on. I think playing along with the rhythm tracks, like you are, is also a great way to work it out.