About 200-300 miles after 600m run-in service on BMW r1200rt experienced very rough / surging idle. Problem went away for a while but then came back with a vengeance. Bike is almost too rough to ride and has died several times with clutch in or while in neutral. Extremely rough, surging idle. Will have to take to dealer, but am curious about cause.

SOURCE: bad battery

Don't rely on on whether the bike will start at a gas station to determine if the charging system is working. Get the multimeter out and do a proper test. Should be getting about 14.5 volts @ around 3K RPM. It's too easy of a test to to just skip. If it is charging then start looking for something else. Was the new battery properly charged to begin with? Loose battery connection? I suppose the GPS could be too much but you said that it was dying last november, so I would suspect something else. P.S. you need a properly charged battery to get an accurate reading for the charging test.

SOURCE: Engine noise at idle speed

Sounds like it's time to adjust the valves. The noise you are likely hearing is due to valve train noise. I suspect you have loose valves. Also I would recommend making sure the carburetors are synchronized. If one side is off you will actually feel a roughness in the motor especially at idle.
When you remove the valve covers be sure to look for any dryness in the valve train. You want to make sure you're not having an oiling problem.
You'd be well off to just do a major tune up. Be sure to replace the spark plugs too.

SOURCE: 2006 r1200rt engine cuts out during hard. bike works fine during

Hi..my name is Keith..and most new motorcycles has a thing called a "Rev Limiter"...and it if you push or rev it hard..it will make all kinds of popping and crackin noise and you will lose horse power..i dont know how hard you are trying to push your motorcycle..i hope this helps you

SOURCE: What causes premature wear in the rings and bore of BMW K75s?

the K75 has very reliable engine .. its unusual for it to fail in this way .. the frozen rings would suggest overheating and thats possible if the radiator fan fails (that happens often before your 80,000) .. many of the pre 1990 k75s would smoke after storing for awhile .. that was a ring gap positioning problem .. that was corrected in newer models .. the smoke however would not have damaged the cylinders .. maybe in the extreme could foul a plug .. is it possible that someone put something in your gas tank ??.. or could it have been run without oil/water or perhaps the wrong type oil (like transmission fluid) ... that engine should have lasted longer than most cars .. nice smooth bike ..

SOURCE: BMW R1150GS 8 years old, 5700 miles. Trouble engaging 1st gear

It's a problem thats common in the Adventures and I think it has to do with the driveshaft set up. I generally let clutch out slighty when kicking it down to 1st and that does the trick. I dont think there's anything mechanically wrong, just one of those glitches in the design.