I feel your pain. Just went through this a couple of months back, and it can certainly put fear into you. It's not the type of thing you can ignore, because it will repeat itself at an inopportune moment.
Do a search for "bike runs wide open" to find a thread where a few of us went through the possibilities for surges and sticky throttles. I got mine sorted out, but I can't honestly pinpoint what caused the problem and which of my fixes solved it. It can be as simple as water in the float bowl splashing up and causing fuel starvation, or as nefarious as a worn throttle slide. Don't discount other air leaks, like at the spark plug (mine was loose enough to turn by hand) or crud or air filter goo in the reed cage. And yes, if your breather tubes are hanging down to collect mud or are routed incorrectly and pinched, you can get a surging effect. A plugged fuel filter will restrict peak fuel flow, and there's always the possibility of bad fuel or water in the gas tank.
There are probably a dozen potential causes of this condition, but if you have a clean carb, new cable, clean and functioning reeds, no air leaks, a throttle pulley with no kinking, and gas that hasn't been contaminated with water or weird oil ratios, then you should have flushed out the problem.