Bruce:
Sorry, I didn't realize this was a brand new installation.
IMHO, running the engine a LITTLE lean shouldn't cause it to misfire. If anything, it will cause it to run HOT but it should still run without misfiring. However, if your plugs are running towards the white side, this is a relatively sure sign that the carb is running lean and that's a relatively easy thing to cure. I believe Holley recommends changing jets by two sizes per attempt, then when the best setting through this iterative process, try one size on either side to arrive at the final jet selection.
Not to beat a dead horse, but the power valve can be a source of some odd problems. In an earlier thread, I stated that I believe it is helpful to have one of the power valve testers which are available through Jegs and Summit. It costs about $40 and you have to get a small hand vacuum pump to go with it, but it allows you to verify that the valve is opening when it's supposed to and will eliminate the valve as a source of potential problems. I check the valves I put in my carbs because I have found them off by as much as 4 inches from the rating stamped on the valve. This can lead to an assortment of little problems. Of course, you can also just get a couple of replacements (about $4.50 each at the speed shop) and just swap one out to see if it makes any difference. Word of advice here: get one of the special tools to remove the screws which attach the metering block and secondary plate to the carb body. If you try to remove them with a standard screwdriver, you'll be successful the first three or four times before you strip out the head of the screw. It's a bear to remove them after you've done this (data point accumulated on this one).
What type of ignition system are you running? I know Mr. Parham likes to use his modified Ford system. Since it is a new engine, there is always the possibility that there may be an infant mortality problem with the ignition system which didn't show up while Southern was running in the engine on their stand. Again, Bill would be the best person to check with to determine any troubleshooting procedures for his modified system.
If you are running an MSD system, they have troubleshooting procedures on their website:
www.msdignition.com
and click on Troubleshooting.
I assume the other ignition system vendors have similar information posted on their sites.
Hopefully, once you get the mixtures set up correctly, that will resolve the misfire. If not, I would start looking at the ignition system itself. My $0.02.