Interesting. Pastor Jack has a similar problem recently, searching for vacuum leaks had him in fits. See this thread: http://www.bmwlt.com/forums/showthre...=vacuum+leakHe
reset the Motonic using the throttle procedure (see Zippy-gg's post above), but that did not solve the problem. Finally he took the bike out and just ran it for an hour on the roads, and that did solve the problem. I don't know if you did your 700 mile trip before or after using the throttle reset procedure, but if you have not run the bike for any length of time since resetting the Motronic, give that a try.
The interesting thing here is that the idle smooths out when you take off the hose from the pulse valve. As others have said, that hose normally is connected to the charcoal cannister. The pulse valve is operated by a solenoid that keeps it shut until the engine reaches a pre-set RPM (I'm cribbing from a post that David Shealey contributed to the thread above). It opens up to create vacuum in the hose to scavenge gas vapor from the charcoal cannister (in pulses?). Although I don't understand why, I know that some engines have run rough at idle when the hose has been pinched under the gas tank. In your case, it may be that the hose is pinched, that it has a hole in it somewhere (there is a connector farther back), or that your cannister is blocked. The common cure for these and other woes caused by the cannister is a "cannisterectomy," a fairly simple procedure that includes blocking off that hose, removing the cannister, and re-routing the front portion of the other hose that goes to the cannister from the gas tank. Procedures for doing this are in the Hall of Wisdom, or do a search on "cannisterectomy."
So, I'd try, in order, resetting the motronic with the throttle procedure, riding the bike for at least a half hour, both town roads and highway, and doing a cannisterectomy. Good luck.