318: too much cylinder head?

Run them. Don't worry.

The "Whoping 5% difference you mention is small as per the % goes but not I. The terms where it is needed to be understood most. And that would be cubic in ha. Say what you want, reason it anyway you like, it won't matter what you say. Your looking at it the wrong way. The bottom li e is cubic inches and not the percent difference.

You made this mistake twice via the Mag article you referanced.

I read your build up list and the heads will work well and IMO as intended via the parts list. I myself would change that 3.7 gear to something higher like a 4.10 or 4.30 and use a 26-1/2-27 inch tire.

You assume wrongly on the bore notch being needed. 2.02 + 1.60 = 3.62 in a stock 3.91 bore. This is plenty of room even with the space in between the valves. While there is some valve shrouding, it is a low concern issue. You'll never notice the difference if you took the steps and machine work to make it better.

On porting the head, it is my opinion that you would be wasting time and money at this level of performance. While some mags may show a gain in power, with such moves, the important part your missing (or the mags as well) is actual road feel and manors in How the engine actually a te and feels.

I have run OOTB Edelbrock heads on a 360 with not much more cam into the low 12's.
(With a 4spd and 4.10's, 27 inch tire.)
Have the heads checked out and cleaned up. That's all you'll need.