Yes, I did do that radius as you suggested Joe, quite a while back in fact. The manifold looks pretty good on the inside.
Tonight I ran the last pulls on the engine, this time with the 1" plenum spacer installed. It didn't really do much good; here's the before and after data. The red lines are without the spacer, and the black lines are with it:

Given no real advantage, I'm going to remove the spacer because that will keep the intake setup from sticking out of the hood so much. I also did some investigations on the crankcase vacuum over the last few days, including pressurizing the crankcase, and didn't find any real significant leaks. The ones I did find I was able to seal up, but even after that I'm still pretty far away from where I want to be for crankcase vacuum. The peak I saw on the dyno runs tonight was about 8 inches, and that was sporadic; during most of the pull the vacuum was only about 4". This is actually pretty disappointing, because I was counting on the Peterson pump to deliver 14-15 inches of vacuum in the crankcase. There's 20 HP there for sure, but I'm not seeing it. Either I have a vacuum leak I don't know about, or that pump is not working like it should.
The major issue I see right now with the engine is the idle speed. I fixed several problems in this regard over the last week and a half, including a throttle linkage issue and a couple of minor leaks in the intake manifold, but despite this I've been unable to get the engine to idle down much below 1500 RPM. It just flat dies at 1300. This is a lot different than the other EFI engines I've worked with, and the cam is not a lot more aggressive than the one in my big SOHC, which idles at 800 RPM. Maybe it is the intake manifold, or maybe I have more tuning to do, or maybe the engine will idle better on pump gas. Or, maybe its just going to be a high idler, which will make it real tough to live with on the street

I'll do some more tuning on the engine in the car and see what happens.
After running on the dyno tonight Steve and I got the motor off the dyno. Joel and I will be assembling the trans to the engine tomorrow night, and Saturday morning it goes into the Mach 1. I'll post some photos of that in my Drag Week blog later this weekend.