Had a hunter ceiling fan that was only working on low. Was using with a 3 speed wall switch the built in pull switch was kept on high.

Removed the built in switch and little black box from inside fan. Now works great but fan seems to turn about 50% faster than when new on high. My question is if anything I did will cause a dangerous problem??

I, personally would not leave it as such. Field modifications of UL listed fans is not a good idea. Either the controller or the fan probably needed replacement.