I did turn the fuel screw in abit to see if that helped it to start, but it seemed to back fire more after that.
That makes it leaner on a four stroke, but you've got it figured out anyway with the no clearance on the intakes discovery.
If a bike starts fine, then suddenly won't start the most common thing is a clogged pilot jet. A new pipe may require modified jetting, but not so much so that it's suddenly hard to start.
Besides a clogged pilot, if the bike in question is a modern, high performance,high compression, high rpm four stroke with some hours on it that's all of a sudden hard to start it can be just what you found, it needs a valve job. Doug