I know there are winds and other effects at very high altitudes but how high can storms with lightning and rain be?
Bottom line, let's say you are flying a craft with the ceiling of a U-2, can't you fly over any storm?
Severe convection will have anvil tops at the tropopause and overshooting tops can penetrate much higher (severe thunderstorm warnings often use a value of 60,000 ft for threats to aircraft). How high the overshooting tops can get is a balance of the positive buoyancy during parcel ascent against the negative buoyancy once it gets into the warming stratospheric air.
A U2 could overfly these storms, but most aircraft are not designed for stratospheric flight (due to the temperature increasing with height in the stratosphere) and any commercial aircraft will be unable to go over these storms.
No. Sprites, also known as upper atmosphere lightning, occur from 31 to 56 miles AGL. (source: Wikipedia) So weather phenomena routinely exceed your U2's altitude by a lot!
Now are Sprites dangerous to flight? Unknown. I know of no case where an aircraft has been hit by a Sprite.