power windows after cooling off

There is a horn relay, but that's after the point power supply.  None of these have relays feeding them.    The fusiable links supply power half and half to the systems and fuse box.   There are only two of them.  So if one was blown there should be much more not functioning.   Unless someting is also shorting.  But that's not likely.

It sounds like one of the power supplies inside or on the back of the fuse block may be out of service.   Do all of the fuses have power to them with the key on?  It's an easy test with a volt meter or test light.   See what you have there. 

The interesting thing is, the alarm and horn are constant power supply with the car off.  The cruise only has power with the key on.  I suspect you are looking for separate problems.  Unless you have a common ground circuit that has lost it's connection.