I too found it pretty confusing for a while until I understood the lighting - the shots are marked with different colour lights at different stages depending on what you need to be shooting for (eg. red for jackpots, gold for records, etc). But as you say, shouldn't this be more obvious when playing? I think so... same with the logos and colours there, and indeed the Icarus target... all pretty confusing to follow even after hundreds of games and reading the rules a few times
The top flipper is pretty difficult as a shot, I think it's a shame there isn't a bigger single shot-reward for it at stages in the game - certainly getting the timing right for the ramp (Prem/LE) is difficult, I guess the Pro version is easier to hit the target.
Do you know what version of the code it was at? I think callouts and screen info were improved for 1.02 which might help a bit with understanding what/where to shoot.