Diagnosing cylinder misfire

So we had got the new engine fired up, broke in and was running and idling good. Recently it’s started running rough and appears to be not running consistently on two of the cylinders. Cylinders 5 and 7. The plugs aren’t showing any burn on them. Has good compression, ample fuel, shows spark through the inline spark tester. Initially I thought maybe lost the cam lobes, pulled the valve covers in both sides and cycled the engine with the coil wire unplugged and all the rockers have equal travel up and down. What makes it seemingly odd is that it was running flawless before. Runs the same way with a 600cfm carb avs and with a brand new 800cfm avs (came free with the edelbrock kit). Timing is still the same as when we initially fired it up. Checked and double checked the cap to plug firing order, I am baffled and needing some direction on what to try next.