Don't use VirtualDub
for deinterlacing. It's vastly inferior, Yadif is best available. You need QTGMC, either via Avisynth or Hybrid. VirtualDub
is for capturing, and many other restoration needs. Just not deinterlace, not anymore.
CNR is vastly inferior to CCD (Camcorder Color Denoise).
Some of that other stuff you've done isn't really helping quality, and just padding out the encoding time.
Temporal Cleaner can be good, as can Temporal Smoother, but Avisynth can sometimes offer superior methods for temporal NR. It really depends on the source, I'd nee to see an actual clip sample, 10 secs max.
Your current before/after doesn't have a large difference.
Sample clip needed. Before/after clips, what you've done, would also help show what you mean by "not all changes are positive". But knowing the filters in use, not surprising.