CF1 and ABL can both have a great effect, it depends on the game.
Your 2nd Q, yes it runs "jerky" on a real N64, the framerate is about 20.. 18 i think? i forget now, i've been away for a long time. If you play PC FPS games and come back the N64 you will find many games are jerky - the console simply wasn't powerful and they had to drop framerates to raise number of polygons. :/ PJ does get the framerate wrong in some games, but this is not one of them.
I recommend running zelda on CF2 and ABL OFF (not the default setting) if you have a fast enough system (probably >1Ghz). The fps should not be any different than the real system (or very very close). Otherwise leave ABL on. There is no point lowering CF unless it does make the game smoother (in this case it doesn't).
Hope that helps.