Couldn't hurt to open the air box, pull the filter and blow compressed air through it. You never know what kind of critters have set up shop in your air box. Also, that will give you the opportunity to mKe sure the air box is sealed tight with all three clamps.
If you're getting spark and fuel, it would seem the only thing either missing or you're getting too much of is air. Have you inspected all the air hoses and boots on the throttle bodies.
The frustrating thing about your situation is that if it doesn't turn over and fuel delivery is working, every time you hit the starter the engine floods and you have to wait till it dries out before trying again.
You might be suffering from multiple issues that need to be addressed one by one. But a Kbike with 43k miles is definitely worth saving...it's just a baby. It will take some work fix but odds are good it will run again if you go at it systematically, I'll toss some ideas out there but I am by far not the most knowledgable person here. These are things I'd do before getting into hardcore diagnostics, which hopefully someone else here can help you with.
Are you sure you're getting spark on all three cylinders? If you have the original OEM spark plug wires, they have a limited lifespan and need to be replaced anyway -- if even one of them is compromised that mAy in conjunction with any other issues you have make the flooding worse and prevent it from turning over. Look for aftermarket wires at beemerboneyard.com or euromotoelectrics.com if you want them quick or contact beachcomber on this forum if you can wait for a shipment from the UK.
Check the crankcase breather hose...search that term on the forum to get info.
Unplug the ECU under the seat, spray contact cleaner on the contacts, and reseat.
Put your location in your profile, maybe there's someone close by who could help you out, you never know.
Don't give up...it's actually a pretty simple machine as far as vehicles go.
