Welcome! I am working on a 1959 Lone Star El Dorado right now so I have done some research already on some of the questions you had.
Decal/emblem: They are kinda hard to come by and they are expensive when you do (for OE) I was lucky enough to where my just need to be cleaned up and a new chrome coat applied, but my backup plan was to get these on ebay-
http://www.ebay.com/itm/Two-Lone-St..._Accessories_Gear&hash=item3392b945dc&vxp=mtr
New windshield: I have come down to 3 options for my boat and they are (in no specific order) UPD plastics, a local plastic factory, or make them myself. Because of the shape of yours I would also check out Taylor Made, they have some in a similar style to your OE one and come with everything including the frame (UPD does not as far as I know) We used the Taylor Made one on my last project-
http://forums.iboats.com/forum/boat...-1956-duratech-s-13r-project-pop-can-splashed
OE Color: I dont know about that year, but I know one year it was a mint green top and hull with a white side. IMHO I think that boat would look AWESOME all polished up! It is cheaper than a good paint job too if you have a buffer.
Other resources: I don't know of many, certainly NONE can compete with Iboats- hands down the best I have found. But there is a yahoo group for Lone*Star boats, I tried to join and have been denied twice for inactivity on part of the mod's. Fiberglassics is a good bank of resources too.
Good luck! Sounds like you have a great project, if you need any help don't be a stranger!