First let me qualify my advice, never done this for myself but have helped a few folks through it who bought my stoves.
1. I would put the baro just above the Elbow that transitions the stove flue from horizontal to vertical, that way you can slide the stove out to adjust/check on it.
2. Lots of folks use insulation to seal around the pipe after installing it to prevent air leaks (both in and out), the oval pipe idea sounds good, or you could carefully squash the 6' flue pipe as the folks I have helped did. IMO it should go past the smoke shelf by at least 6" if that gets into the flue then so be it. And no the oval or squashed pipe will not affect your draft.
Have fun, I'm sure others will chime in with their experience.