I've been using the audio filter on CWget and it almost helps. The
problem is that it introduces clicking, cracking, poping, and wheezing
to the filtered sound. Have you experienced this? I've got a very fast
computer and I've tried setting the process priority to "real time"
and the noise on the filter audio output through the sound card
remains. I've tried a number of different sound cards with the same
result.

I'm thinking that if it could run the filter without adding the
garbage that the Morse decoder function would be improved.

Have you tried an PC based audio filter that works better?