My pleasure. I've just come off a project where I had to inundate myself in video stuff, so I'm glad to share the knowledge. And that project was...
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[b]MIDI 101: MIDI Demystified[/b]
OK, to your questions...
Regarding codecs, man, it's such a dark art all of this video stuff. And I'm no expert. But it really depends on the nature of the footage as to which one might work best.
High quality DV renders can look great but the color is sometimes a bit washed out compared to the original. H.264 can deliver great color but sometimes edges (and certain colors) can look blurry. Again, it depends on the kind of material. Sorensen3 is considered a "legacy" codec but can produce a really nice result. If you're game to try that one but you don't have it on your system, you can download "legacy codecs" from the Apple website.
So from my limited experience, I'd say to try DV, H.264, Sorensen3, and Apple Intermediate Codec (AIC).
As far as STP is concerned, I'd suggest getting all of your audio laid up in Logic first. Then, for noise reduction (which I hear STP is really good for), export a file and see if you can improve the sound using STP's plugins. Then re-import that audio back into Logic and continue with your EQ, level, and compression. Always make sure to check sync, though, for any files you export from Logic and then bring back in.