I've got both the Tornado Terry long shaft version and the original version of the Reunion stick. I like the throw of the shorter stick better, but the throw of the longer shaft is very similar to the Happ Super & Competition sticks. It does require less effort with the longer stick due to the increased leverage, but it is okay. I have no doubts that I could rack up Pacman scores just as high with that stick as I do with the shorter stick (I just have a dedicated Pacman cocktail so I don't play Pacman on the machine with the longer stick).
The 1/8" lexan on top is no problem. Remember that these joysticks are made to go under 1/8" metal anyway. I don't think the artwork resting on top of the joystick will be a problem, but you can always fill the top of the joystick base in with some type of filler if you need to. You would have to put the dustwashers on top of the lexan if you did that.