Bad plug wires will definitely cause the problem you describe. I'm surprised that Southern delivered the engine with wires in that shape, but mistakes to occur and I'm also sure Bill had no problem with replacing them for you.
Since your engine is new, some fouling on the plugs will be normal until the rings seat. I talked with Parham after I received my engine and he said it's normal to take about 2000 to 2500 miles for the rings to seat. Bill uses chrome-moly rings, which are much harder than the standard iron rings. Chrome-moly rings do not seat like the iron rings; it's more like the cylinders wear to match the rings than the other way around. I have had a couple of other engines (Chevys) in which we installed chrome-moly rings and they also seemed to take forever to seat. Until they do, you will find some
oil residue on the plugs. MY current engine kept burning
oil until just recently when the #7 ring finally seated. After that,
oil consumption went down to normal and the plugs seem to be maintaining color. For these types of engines, I consider a quart every 1000 miles to be normal. Other opinions will vary, but that's what I use as a rule of thumb. Bill suggests using Valvoline 20W50 oil, and that's what I've been using. I'm debating whether to switch to
synthetic but haven't made the plunge yet. Incidently, my brother tells me that WalMart (the one he goes to is in Buffalo NY) periodically sells 5-gallon jugs of Mobil 1 for around $17. I haven't seen this around here but I'm sure going to start looking. This isn't an endorsement of WalMart, either, I just haven't heard of this at any other store.
FWIW, my engine runs about 10.5 inches manifold vacuum at idle. I'm running a 484 stroker kit, Crane cam and dual 600 cfm Holleys. I hooked up a vacuum gauge from the rear carb, ran a vacuum line into the cab and duct taped the gauge to the dashboard. I then stabilized the car at 1000 rpm intervals in each gear and recorded the vacuum readings. The lowest reading was, in fact, at idle and all of the others were higher. I initially selected a 5.5 power valve based on the old "1/2 of the idle vacuum" rule of thumb and had all sorts of bog-down problems. I went back, bought two 8.5 valves and installed them and the bog went away. Actually, I bought FOUR 8.5 valves because when I tested the first two, they actually opened at 4.5 inches rather than the 8.5 stamped on the valves. This is why I recommended getting a tester and checking the valves before installation. My experience, anyway.