A Quick Answer.
Marquee.
Some of these features are quite new, so most of the people here will not yet have done this. I did #2 with basically 2 pieces of plexi. It needs to be sandwiched between the artwork and then put into place.
I was interested in #4 and I asked Scott some questions about it. It is only 1 piece of plexi and it is mounted to the front. So your artwork will be visible. If you want to have that "reflective" look of being behind the plexi, and the extra protection, you could always get #4 and an extra piece of plexi. I don't know if there is a quality difference between #2 & #4 (even though they are both "ultimate" one has a sticky back so

). However, if you remove the Marquee often, I found it a little bit of a pain to juggle the three pieces, so the sticky back pre-installed might work out great.
Do you need the front piece of plexi? That depends on your setup. I personally like the plexi look in front of the marque, so for me ... yes.
I know Scott told me the width of everything, but I can't seem to remember. I'm "pretty sure" the plexi is 1/8" per piece. and the artwork is really minimal width (few sheets of paper thick).
Control Panel:
No, it isn't necessarily standard practice to use acrylic over the cp top. Sure lots of people do it, but it isn't needed. If you get Scot's stick-on artwork it has a very tough finish and will hold up just fine to most abuse.
To answer your other questions.
Some people use the Black Carrige bolts to install plexi, others just let the buttons grab onto it.
Typically, people like to offset the T-Molding, so all the sides of the plexi fit "in" the T-Molding. The easist way to do this is use 5/8" MDF for the top and 1/8" for the Plexi (tha'ts 6/8 or 3/4, so perfect for 3/4 T-molding). Other people still use the 3/4 MDF, and they just off-set the T-molding up, and round the bottom so it doesn't have an edge.
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I used the "with Adhesive" even though I was using plexi, that's up to you. But Scott is just mailing you the artwork, you have to apply it yourself.
I created my own 300 DPI PSD file, but so long as the artwork is good enough I'm sure a PNG will work.
Your artwork will always go over the tops of everything, nothing is going on top. If you are going to TOP mount in a traditional way, you will need to route out enough of the top to fit the mounting plate in flush. Also, you will need to BONDO the top smooth, or you will get dimples in the artwork when applied (like me

). I suggest you read up on mounting, Top or bottom varying from person to person. I don't suggest top mounting the u360's if you are going to adhere the artwork to it, as you will need to take it apart at some point to re-lubricate it over time.
Most people use 1/8" plexi, not LEXAN.