Greetings
I've been having a devil of a time getting my newly acquired 1999 BMW "Funduro" to run properly and I'm hoping someone can help me out.
The bike was not well-maintained, but I have done my best to clean it up and replace neglected parts.
In its current state, the bike will not run properly below 4000 RPM, so we can rule out any regulator issues.
It will start fairly easily enough (even when cold) but the idle is erratic. If I twist the throttle VERY SLOWLY, the engine speed will increase until about 2000 RPM's whereon it will stop increasing, or may even decrease a bit. As I continue to twist, the engine speed will eventually increase beyond 2000 RPM but there is another point around 3000 - 3500 rpm where it will become erratic again. Once it gets above 4000 RPM, the engine runs well and pulls strong.
When I bought it, the PO claimed that the choke cable was "sticky"...but in fact, it had broken off at the plastic hub and the choke plunger was actually seized inside its bore. Once I got that repaired, I also discovered that the screwdriver slot one of the pilot jets had been stripped, so I had to use a screw extractor to get that one out for cleaning. Since I didn't want to put a broken jet back in, I opted to replace them both but since they are an odd size (#41.3) I went to the next size up which is a #42.5
Float level is set as per the manual.
Mixture screws set to 3½ turns as per the manual.
Main jets are stock #132.5
Mileage is terrible...about 25 miles per gallon (about 10L/100km)
I have been across various forums and Facebook groups trying to solve these issues...to no avail.
One member mentioned that his mileage was bad until he replaced his spark plug boots, so I thought that I might be having an ignition issue, and I replaced ONE of my spark plug boots (I only had one spare).
The other day, I disconnected one of my ignition coils (so that only ONE spark plug would be firing) and started the engine. It ran roughly and needed choke to stay running - this was the "new" spark plug boot.
I repeated the test with the other spark plug (original) and it ran better. So I measured the resistance of the NEW boot and found it to be over 20K ohms...that's too much. The original boot was 13K ohms (closer to spec). I ended up replacing the NEW boot with its old counterpart, but noticed that its resistance was over 4 MEG ohms, so I had to clean it up to get it back to within spec. To make a long story short, I've ordered two NEW plug boots and they should be here within a week or two.
With the two original spark plug boots back on the bike, I was able to start it but it still ran quite rough, so I turned IN the mixture screw on the LEFT side carb, since I can't adjust the RIGHT side when the engine is running.
The further I turned it IN, the better the engine ran...until I reached the bottom of its travel. The LEFT side mixture screw is fully closed and the engine runs "better" than when it is set to factory recommendations. Right side is set to 3½ turns as per the manual.
This is what I find the most perplexing because the ONLY parts which are not OEM are the two pilot jets and I can't see how going up only ONE size would have such a devastating effect on overall operation.

I have two carb kits coming from Holland (hpefully, they will get here this month) which includes new pilot jets (supposedly the proper size), new needles and emulsion tubes, new float valve and seats, and new slide guides. If this doesn't get it working, then I am really at a loss as to how to proceed.
In summary:
Factory recommended settings make it run worse.
Only non-OEM parts are the pilot jets.
Floats are properly set and are NOT water-logged, each one weighs 7g.
Fresh fuel.
Fuel flow is good and strong...no blockages anywhere.
Engine speed will hang at 2000 RPM and dropoff, when gently accelerated.
Engine runs well above 4000 RPM but mileage is terrible.
No tears, holes or leaks in carb manifolds when installed.
Air filter is clean.
Valve timing has been checked and valve clearance is good.
SPark plugs are new, although the boots are suspect and will be replaced.