Well, I was hoping you would come up with some 'original' interests of yours, you just commented on those I listed. Though this already helps a bit, I'm still uncertain about what you actually want to do - fortunately, there seems to be enough time left to sort this out ;-)
From my experience with this board, most of those who come to Germany are mainly interested in romantic castles, small towns with half-timbered houses etc. Yet alone the size of Germany makes it difficult to build up a route from this alone: After the obvious Middle-Rhine-valley (+Mosel valley), you could take a southern route (towards the Black Forest), a south-eastern route (towards the Allgäu, incl. Neuschwanstein), an eastern route (towards Franconia), another eastern route (towards Thuringia), a north-eastern route (towards the Hatz mountains, with places like Quedlinburg) etc. etc.
I think you're getting the drift now: All these would fit your criteria, yet obviously you cannot even 'cover' half of them in the amount of time given. So do some research and work on your criterias, come back and discuss details and hidden gems.
As a rough guideline, you should plan on staying at least 3 nights in a place/area (unless it's merely a stopover) in order to really appreciate it, or your honeymoon will turn into a hectic whirlwind-tour.
So for the moment, I will return to your original questions:
-
Agree with marcopolko, the Shell maps rank among the best for Germany (as much as I like Michelin maps, I think they're still publishing Germany 1:400.000 only, which is less than ideal for exploring the countryside), yet for a rough planning beforehand, [www.viamichelin.com] is still the best source. Hiking maps (1:25.000-50.000) will be available at local tourist offices/bookshops. Personally, I have a deep mistrust in GPS navigation systems, yet I admit that it's thoroughly irrational.
-
The German Tourist board has established a long list of 'routes' in Germany that link places of interest. Note that sometimes the routes aren't scenic but for the towns.
-
Though physically this could be done, IMO you'll spend too much of your precious time on the road (e.g. Prague back to Rotterdam is nearly 1000kms). Save it for a separate trip (or maybe long-weekend + budget flight).
-
I doubt there's a problem here. Most hotels offer parking (mostly free of charge), navigating smaller towns isn't that difficult and in rural areas, you'll need your car to get to the town centres anyway, so you may just as well stay there. As June is just before school's summer holidays, a lot of places will already be busy, yet not to an extreme. Expect a lot of school-classes on tour (especially Prague).
One last point for now: You state that you want to go by your own car and ferry over. Is there a special reason why you're doing this? A quick glance at the P&O-homepage tells me that the transfer will cost you 500,- Euro at least + 2x800kms travel to/from the harbours, which would be another 200,- Euro in fuel costs. For this money, you could easily get a cheap flight to e.g. Edinburgh-Cologne (Germanwings) or Edinburgh-Hahn (Ryanair), both of which would be ideally located to start your holiday close to the Rhine, and get a rental car. You'll save precious time, too.
Further, in case you consider the rental car, check one-way-rentals (often free of charge when dropping inside one country, hefty charge when dropping in a different country), so you won't have to backtrack too much. Check a page like [www.whichbudget.com] to establish the availability of budget flights to/from places. In case you still want to visit Prague, consider a one-way-rental inside Germany, drop off the car in a place like Nuremberg or Dresden and continue by rail, return to Edinburgh by plane.
Just some ideas.