MV17,
I will try to answer as much as I can, forgive me if I overlook something.
1.) Military members vehicles are not subjected to the same standards, except where noise is involved. Here is the UN document on how they test and what levels
http://www.unece.org/trans/main/wp29/wp29regs/r041r1e.pdf Basically, run RPM half way to redline, measure dB, validate not over threshold.
Stock US pipes are fine, a budy of mine just bought the 110 CVO RK. He had to take the pipes off new bike and put on 2003 - 95CI Ultra to get it to pass.
The AirForce and Army have one testing station in Kaiserslautern, with a dB meter. DON'T SELL YOUR STOCK PIPES, YOU WILL NEED 'EM. Bayern, Germany is renown for the control on loud pipes by the Polizei. If you can't fix the noise on the side of the road, you could get impounded. A company in Belgium makes some really cool pipes with electrically actuacted butterfly valves that you control from pusbuttons added to the handlebars; expensive at nearly $2000 now. 95db is max, above and beyond what UN document allows, but they give you some space for wear and tear. I am not sure what German law is, but many European bikers tear off the stock pipes and put on louder ones. But they always keep the originals for bi-annual inspections.
Don't worry about marker lights, or fog lights, or blinkers, you are a military member of US Armed Forces who will be exempt from excrutiating German guide lines. Another one of my friends had the same lighting set up you have and he passed inspection. My friends and I normally run with the spots on, because we are more visable. Some drivers coming from oposite direction hate it, but that's about it. I have never gotten stopped for running with them on and I have over 26K miles driving my '04 Eglide in Germany. Plus all of my friends have never gotten stoped or warned or anything.
Your warranty service will need to be performed at a local German Harley-Dealership. There are lots of them here in Germany. If you are talking about car warranties, you will need to check the fine print and find out if your car is covered world-wide and under what conditions. As far as extended warranties go, you will have to read the fine print. Most extended warranties are provided by third party companies and they are not worth it, many will give you a refund if you haven't started it; i.e. factory warranty still good. As I just bought my 110 CVO, I ordered an extended warranty through AAFES. Also, you might be able to get an extended warranty through AAFES for your stateside purchased bike. Aprox. $1200 for three more years. However, for all extended warranty work, you pay upfront and submit claims, each claim carries a $50 fee. So if something small is broke, wait until you get many small things broke and submit under one claim.
TIRES - They are NOT square here. I know the stock Dunlops have been driven up to 110 MPH by individuals I ride with. But on any E-Glide, that is scary fast because of the buffeting going on. As I haven't gotten my new CVO yet, 10 days and counting, I can't say how fast it goes or what it feels like, but my '04 Ultra ran 100MPH and it felt bad in long banking curves.
The sweet spot on the Autobahn for an Ultra is around 75 to 85 MPH. You can occassionally go faster if you need to, I just never saw the need, PINS and NEEDLES, and WHITE NUCKLES above 100MPH. The fastest I have ever gone on the Autobahn was about 175MPH on a bike made on an island in the Pacific Ocean. :-)
Enjoy your time while you are in Germany, if you come to the Kaiserslautern/ Mannheim / Heidelberg area, you can ride with our group.