mil, yes
Great, that'll make things a lot easier.
1st, get to the auto hobby shop on base. MWRS is supposed to staff each one of them with at least 1 qualified mechanic who's there to advise you on what you're doing and how you're doing it - to include using the tools in the shop. So, go and talk to them about the changes you're going to be making. No, they aren't bike mechanics and definitely NOT HD mechanics BUT they are experienced and competent with basic procedures that are common to most motor vehicles and that would include exhaust work. I have no doubts that between the collective advise from this site and the help you can get from your hobbyshop mechanics that you'll be able to make the exhaust changes that have been listed earlier.
2nd When I was stationed in Germany, we had to get vehicle inspections (to include emissions testing) done by the Germans at one of their inspection stations. This was a one time requirement in order to get your vehicle registered and licensed. The reason I bring this up is because you need to make sure that any changes you make will be legal/acceptable to your host nation (again the hobbyshop mechanic MAY be helpful BUT he/she is NOT the final authority on this - the tester will be). If the mods are not legal there then you will need to find out if the inspections are still being done and if so, are they a one time only or are they annual or whatever. If the inspections are one time only for your entire tour then you could conceivably make your changes AFTER your inspection. I am NOT condoning the violation of laws and/or international agreements - I'm merely pointing out that it may be an avenue someone so inclined could pursue.
3rd make sure ANY AND ALL changes you make to your bike are NOT going to prevent you from bringing it home with you when you eventually DEROS. $30K+ is a LOT to drop on anything and it would suck to not be able to bring it home when it's time to PCS. Of course another way around this would be to make sure you can return the bike to original condition quickly/easily/inexpensively prior to move.
4th (and last) Find a riding group that you are comfortable with. Hang out with them, get to know them, pick their brains on your ideas/options. Find members on this board that are in Germany (Kraut is a member here that is in Germany) - they'll be able to assist you in finding groups to get to meet.
Good luck and keep us posted.