I think I finally found a promising lead in the case everyone. After reviewing this thread:
http://forum.cakewalk.com/CPU-Core-1-Maxing-Out-m3366417.aspx - I went into the Config file and set the MMCSS ThreadPriority to a value of 2. My understanding is that this gives SONAR access to an extra CPU processing thread on quad-core and above systems, but I'm not a developer and couldn't explain it in proper technical terms. Could someone give a more thorough explanation?
Anyway, the situation with Rapture Pro has improved as a result. I was able to set the audio buffer to a more respectable 128, and the pops seem to have gone away. I'm still testing it out but this is much better than before.