I'm not going to be able to help much with this one. I know absolutely nothing about the navy of 17th-century Hamburg. I do know that the Wappen von Hamburg is quite a popular model subject - especially in Europe. I'm not sure why that's the case. The fact that there are so many models of her suggests that there's either a good, detailed set of contemporary plans or a good, detailed contemporary model of her in some archive or museum somewhere. Michel - can you help?
Her overall shape and look are those of a ship-of-the-line, but she usually seems to be referred to as either a "heavy frigate" or a "convoy ship." Actually that makes sense. The word "frigate" had a much broader meaning in the mid-seventeenth century than it did later, and I gather she spent most of her career escorting Hamburger merchantmen around the Baltic and North Seas. I imagine the warship fleet of Hamburg was too small to form a line of battle.
Taubman Plans Service ( www.taubmansonline.com ) offers a set of plans for this ship, but they're quite expensive. A Google search, however, turned up a surprising number of references to her. The best I found is this: http://www.all-model.com/list1/hamburg/hamburg.html . It's a set of small-scale, but well-rendered plans. There are five separate drawings: a set of hull lines, an overall outboard profile (including sails and rigging), a sail and running rigging plan, a standing rigging plan, and that rarest of all finds: a belaying point plan. The originals presumably were in German, and a few of the names of rigging lines are garbled a little. In general, though, these look like nice drawings - quite useful for this particular project. They can be printed out directly from the website.
At the top of the page is a button labeled "Heavy frigate 'Wappen von Gamburg [sic]' Free download." I clicked on that with considerable enthusiasm, but the results weren't satisfactory. I was invited to save the download to my hard drive, and spent about five minutes waiting for that to happen. The computer told me it had saved the file, all right, but when I tried to open it I just got a mass of question marks. I guess I don't have the necessary software program. I'll try it on the office computer tomorrow. Maybe a member who's more of a computer whiz than me can help. (Michel - are your there?)
Since the two sail plans both show the sails set, they also show the yards in their raised positions. Unless you give the model set sails (which I don't recommend), I strongly recommend putting the yards in their lowered positions. On board a ship without sails (or with her sails furled), the lower yards, the spritsail yard, and the big lateen yard on the mizzenmast would stay in the positions shown on the drawings. The fore, main, and mizzen topsail yards would be lowered to a foot or two above the lower mast caps. The spritsail topsail yard also would be lowered to the cap, and the fore and main topgallants would be lowered to a foot or so above the topmast caps. People who've spent a lot of time looking at ship models will tell you that a model with lowered yards looks a great deal better.
That Google search turned up quite a few photos of models of the ship. The quality of those models, however, varies considerably. (Beware of anything built from a Corel wood kit. There seems to be a fairly general consensus that of all the continental European plank-on-bulkhead kit manufacturers, Corel is, in terms of historical reasearch, the worst.) Quite a few photos of Wappen von Hamburg models also are posted over at the Drydock Models website. The quality of those models also is variable, but they'll give some idea of how other modelers have handled the color scheme.
Darcy Lever's Young Officer's Sheet Anchor is a great source for ship modelers. Do remember, though, that it deals quite specifically with the British Royal Navy, and dates from the late eighteenth century. (Some modern reprints contain updates that cover changes in practice through the mid-nineteenth century, and in the merchant service.) Don't be surprised if Lever's information conflicts with the rigging plans of the Wappen von Hamburg.
I'm inclined to agree with cthulhu about red paint on the decks. It's not totally inconceivable. Red was a popular color for interior woodwork on board ships of the period. (The traditional explanation is that the red was intended to camouflage blood, but recent research has shed doubt on that. It seems more likely that red paint was simply a good, affordable, reasonably durable and waterproof primer.) Eighteenth-century British ships often had red orlop decks. (H.M.S. Victory's orlop is painted red.) And I think I've bumped into a few other references to red deck planking - especially in continental warships of the seventeenth century. But the idea of red weather decks in a big ship like the Wappen von Hamburg seems pretty bizarre. I certainly wouldn't paint the decks of such a model red unless I had considerably more evidence than a Lindberg instruction sheet.
I agree completely with those who say you don't need an airbrush for this sort of work. I've got an airbrush, but I rarely if ever use it on sailing ships. (Come to think of it, I rarely use it - period.) I know some people do like airbrushes for this kind of model, but to my eye an airbrushed finish is simply out of place on a sailing ship. I also think a good brush technique is an essential part of the arsenal of anybody seriously interested in sailing ship modeling - even if he or she does use an airbrush for some purposes.
Primer isn't necessary to make modern hobby paints stick to styrene. Using a sprayed coat of grey as a basis for a white finish coat is, however, an excellent idea. Modern hobby paints give excellent coverage, but covering dark brown plastic with white paint remains a challenge.
There are no "right" or "wrong" shades of color in this part of the modeling world. (Thank goodness.) My suggestion would be to take a look at some of those photos of other modelers' Wappen von Hamburgs, and combine their ideas about colors with your own taste. It may have been established that the ship had dark green trim, but nobody's going to tell you that a particular shade of dark green is "wrong."
You might want to look into the range of acrylic paints sold by Model Shipways (available through Model Expo: www.modelexpoonline.com ). Those colors were formulated specifically for sailing ships, by people who knew what they were doing. The Testor's "Acryl" line also includes some sailing ship colors (including such things as "Hull Tallow," which would look great on the bottom of a ship like this one). Unfortunately not all Testor's racks include the ship colors. (The one in my local hobby shop doesn't; the nearest shop with a full range of Testor's colors is more than a hundred miles away. Sob.) But if your local dealer has them, they're certainly worth a look. If not, don't despair. As you've suggested, the ranges of paints formulated for aircraft, tanks, and cars has plenty to offer the ship modeler.
Hope this helps a little. Good luck. That kit has the potential to produce a fine model.