More thoughts on this:

When the radio shorted out did you have to re-enter the security
code (that would indicate all power was lost)?

I also recall that the battery ground wires are a weak area and
should be checked to make sure you have good connections. A bad
ground can cause all sorts of electrical gremlins.

Any recent service or event preceeding the problem (like cleaned
the engine or had a new stereo installed or service)?