I made the thruhiker jacket last winter. Very great pattern and instruction booklet, I highly recommend it. I would do sew through baffles with your estimated loft. I would also think you are spot on with 3 oz of down. The pattern comes with 5.something and you can buy an extra .5 oz of down to basically bring it to 6 oz. I have 3" loft around the body and 1" around the arms and head (I added a hood which was why I ordered the extra .5 oz of down, should have put this in here the first time). About 2-2.5" if you averaged it out is what their website says. I would either shoot Tim and enlightened equipment an email or pm about karo step clothing. There was a thread a few months ago with great detail about karo step. I believe he was going to try a jacket, I am about to try it with a pair of pants based on that thread. I have no clue if he made his jacket yet, but my pants won't be done for 2-3 weeks and they won't get decent testing for about 2 months.
Good luck if you try it, and post how it goes.
I would start by finding the MYOG thread from a few months ago with detail about karo step.