Definitely ask for the magnesium wheel upgrade. Well worth it.
Inside joke, sorry.
The big tank isn't necessary. The standard tank is 30 gallons, which seems like more than enough. Get the bigger brakes. Get the Avon tire upgrade if you feel like spending extra money, certainly money better spent than on the stainless steel frame upgrade, though everyone is different in their likes and dislikes.
I'd have them cut the holes to the sidepipes and definitely get the wheelwell foam, though you could do that if you're the industrious type.
I also think the non-adjustable shocks are great, but I've never felt how the adjustable shocks feel, but I believe most buyers opt for non-adjustable shocks.
Then there are the exterior finish options. Filed, Brushed or Fully Polished. Center stripes or no center stripes and also there are the team stripes for the front fender. If you paint your car, then the Filed finish is free. The other naked aluminum options are really your individual preference. Each finish has its fans.