I built a 360 I planned to boost but am giving it to my folks instead, but I did have the chance to dyno it. It's a .030" magnum block, magnum R/T heads, very mildly ported with 2.00"/1.55" valves (LS1 stock valves, aka free), a comp hydraulic roller with 216/224 @.050 and .534" (.501" with 1.5 rockers), 114 lsa installed at 110 icl, edelbrock rpm air gap, 750 Holley DP and 1-5/8" primary tube headers. Powering the water pump and alternator as I was too lazy to take them off for the dyno, it put out 388hp with 31 degrees total timing. I had the rings gapped extra for boost and have KB inverted dome pistons in there giving about 9.0:1 cr. Killer flat powerband and I expect it'd make 500 with 6-8 lbs of boost. Won't likely ever find out now as it's going into a 2000 Dakota 4x4.
Point being, this engine, designed for (light) boost, makes more power N/A. I think I would iron out the engine minus blower first, then go from there. I definitely agree that the heads are killing it. I doubt they flow over 200 cfm, and if they do, it isn't by much. My R/T's with the light buff I did were flowing about 240 at peak lift. After the freshen I did more extensive work with 2.02/1.60 and got them up to 275 or so. No dyno numbers now unfortunately. I'm less concerned with exhaust numbers. I do like to have as good an exhaust as possible, but I won't worry about the exit until I have all I can get out of the entrance. The exhaust will get out, it has to, it has nowhere else to go, but the more air you can cram into it, the more fuel you can burn and the more power you can make.
Looking back at this post I wonder if anything I wrote will actually help...