2000 honda cr250r running full RPM?

I have a 2000 honda cr250r, one day i went to start it and it started up idling what sounded like full RPM, it was screaming like crazy, kill switch wouldnt kill it, managed to put it in gear and drop the clutch to shut it off. Started it a few days later and it was fine, then just the other day i was riding and hit a small jump, when i landed the bike took off and i fell off the back, it drove on its own for a good 30-50ft until it fell over, but while it was leaning on its side it was idling at the full RPM again, and couldnt get it shut off with the kill switch. Went to start it a few minutes later and same thing happened with the bike screaming at crazy high rpm, my buddy did a few adjustments to it and it seemed okay enough to drive it back to the truck and bring it into the shop, my reed boot needs to be replaced because of split in the rubber, but i can't figure out why this would have happened, and want to find a solution because its scary as hell when it happens and is dangerous

Has the throttle cable been cleaned and lubed?
Has the throttle grip been cleaned and lubed?

Hey, it's a DIRT-bike and dirt-bikes get dirty for some reason.

Ever thought about fixing the kill switch?

I think you'll find that the hole in the intake rubber is likely to be causing your woes. Fix this before spending time or money on anything else. It will make the bike run too lean and cause big (expensive) problems, and is probably the main issue here.

Next, check to make sure the throttle isn't sticking. With the bike started and running at a low idle (if you can achieve this) turn the steering left lock to right lock and make sure that the RPM doesn't increase when you do this. If the RPM increases when you turn the steering, it means you have a throttle cable routing problem. Re-route the throttle cable so it doesn't bind.

A crack in the boot will cause a lean condition, and that will cause the problems you describe.

Sounds like jamming throttle cable - Air leak in inlet stub won't cause very high revs, more likely won't idle at all.
Also get your kill switch fixed - it's a safety device in case you drop the bike on yourself (or your over revving happens again)

An air leak at the intake manifold will cause a 2 stroke engine to rev wide open.
The slit in the reed boot is enough to cause your bike's dilemma.

If you ever have that problem again - quickly turn on the choke.
The air leak will create an over lean fuel mixture.
The additional fuel, let in from the choke, will balance the mixture and stop the reving.