I seems like my major issue was that I was editing on an HDV timeline instead of Pro Res. I changed it to Pro Res and everything seemed to run pretty fast. I got answers from Shane and someone else on an Apple forum:
…and when I said I used “it” previously, I was referring to Neat Video. I have also used the other filters quite often, but not as much Noise Reduction as I did on this project.
I did use it previously, but not throughout a whole project as I had on this one. Do you think it’s that render intensive that it would cause my machine to bog down with its capabilities?