I recorded a .wav file  that had millisecond sized gaps  in the track or clip (I'll call them hiccoughs).  After importing  the clip into Sonar X3 I spent quite a bit of time carefully removing them by manually deleting the millisecond void sections of the track. I can't help but believe that there is a better way that has been devised by the Cakewalk engineers to automatically make those corrections.  Is there?  If so, what is the process?  I thought that the "Deglitch" feature would probably work but haven't managed to figure out how!   

Waves X-Click & pops or Sony interpolate

Sorry. Not sure what you are suggesting.  Are they pieces of SW?  

If you have access to Adobe Audition, there's a delete silence Filter (in CC: Filter/Effects/Diagnostics). You could run the clips through this filter first.

Have you tried the "Removing silence" (Process > Apply Effect > Remove Silence)?

I doubt if the Remove Silence -feature is any good for  glitches that are only a few milliseconds long(?)

I believe what your asking is not possible to do yet in sonar,
those things are typically done I isotope RX, Waves x, and other programs made for the job.
ive seen a few suggestions before but nothing that has gone in my book of, this works great.
it was always some band aid that sound sounded like dung
.
 
this is true to the reason you hear many folk say "its a good way to ruin a track.
because if it was fixable, it wouldn't be ruined, sorry.