Ed,
   I have an identical set up to yours (much faster than Bill's) and
have flown in the rain but not near the freezing level.  I typically
only open the Alternate Air when off the ground and it is usually the
first thing I close to start a decent.  
   I do agree with you that the probable cause of your loss of MP was a
frozen filter.  Freezing level 4K, you started to notice rough engine at
6K and did not enjoy a normal one until you passed through 4K again.
   You did not elaborate on the intensity of rain on your departure and
climb out.  Was it uniform throughout or just intense below 4K?

Hollis Helms