@Moxy No, I don't really have the patience to do that. I'll do the upscaling, cleanup, and resampling in a single pass, and just let it run overnight. I'd be afraid of introducing too many artifacts running multiple passes, but it seems like you're getting decent results. I do the final cropping / cutting / encoding in a separate program (TMpgEnc) that gives me a bit more fine control, but that's about it.
Version 3 of Topaz Video AI is significantly improved from Version 2, but it seems like overall stability took a pretty big hit. There are some blocking issues with some movies I tried where I just can't proceed. In these cases I'll just wait for an upgrade and hope for the best. Fortunately these issues are becoming more rare with each new patch.
Overall, been pretty impressed with the quality. Not quite the same as true HD quality, but older SD movies are so much more watchable after being processed. I'm slowly going through some of my favorite oldies from the 2000's and sharing the results.