OK, so finally the noise is gone.
What a mission. After installing a new CCT, I wanted to change the oil and discovered that the oil drain plug was stripped. There is not enough space between the frame and the engine cases to use an easy-out, so I had to remove the engine, which is quite a mission.
That engine fills up the chassis so much so, that it is impossible to remove all the dirt without at least taking off the tank, and cleaning the engine and wires by hand. When I bought the bike, it looked fairly clean, but upon stripping it, and removing the engine, I could not believe how dirty it was. The first owner rode the bike where there is that super fine dust, which gets in everywhere. You cannot believe what mission it is to clean that dust off the cables and connectors. You basically have to scrub each cable with a toothbrush with an alcohol based solution. I had to use ear buds to clean the connectors, of which I did a pretty crappy job at best. Its just plain impossible to remove all the dust and dirt.
Once the engine was removed, I figured that I might was well check the valve clearances, timing chain and chain rail/guide, as was suggested on this forum and by our local KTM wiseass. When I started removing the cams etc, I thought I might as well check the top end, con rod etc, especially after noticing how dirty the inside of the bike was. So further down the rabbit hole I went. I was really worried that I ended up buying a bike that will cost me more to fix that I paid for it. I don't have much mechanic experience, and this was the first 4T I ever worked on, so it was quite confusing/scary at best of times.The piston ended up being fine, and it was suggested by an experienced mechanic/friend to just replace the cam chain and the piston rings after I took the engine to his place to have a look at it. The CCT rail and guide was fine. The Maccie also said the bottom end was still good. After 170 hours, the valves were bordering on the high end of the tolerance range, so I put larger shimms in as well.
Quite a few stripped bolts and threads here and there, and waiting for parts most of the time, I finally put the bike back together. After quite a struggle with getting the tank back on, and removing the right radiator retaining bolts at least 10 times, the bike was ready to start.
Click click nothing..... My worst nightmare came true. And worst of all, the FI light bulb was done, so I could not even get an error message from it. I checked and checked and checked everything again. Removed all the electrical connectors to make sure the contact cleaner evaporated completely. Checked the spark plug(partially remove radiator again) to make sure it was producing a spark. I then thought I might have messed up one of the connectors, or perhaps broke a wire in the stripping/assembly process. Later that afternoon I was back in the garage, hoping to find the culprit, before I had to resort to taking the bike to the KTM agents. After quite a long time of searching, and nearly cancelling my date for that evening, I found that one of the plugs that connect to the FI unit was not plugged in :-|
Plugged it in, pressed the e-start button and KABOOOOOOM! Followed by thousands more KABOOOMS! The bike was running, and I had my happy ending 5 hours before my date arrived