2005 Chevy Silverado Flutter when accelerating

Original question: Engine problem
2005 Chevy Silverado V8 Four Wheel Drive Automatic 40000 miles

I recently installed headers on my Silverado 5.3L. Around the same time, I also replaced my spark plugs and wires. I also installed a tuned chip. At first everything was great, I then started getting a fluttering noise after a couple of weeks. At first, I thought it was a gasket leak. I retorqued the header bolts to specs, and the collector bolts as well. I still have the noise. It only occurs when I'm accelerating, or the engine is under stress, going up a hill for example. Could this be a valve issue?

FOLLOW UP QUESTION:

Here is my set up. 5.3L engine, no EGR, no A.I.R, K&N FIPK cold air intake, Granatelli cold air tuned MAF, Doug Thorley headers, Magnaflow high flow catalytic converters, Magnaflow catback exhaust single in dual out. I wouldn't think I'm suffering from back pressure issues. I'll check the backpressure, but if that is good, is there something else that could be causing the issue?

Is it possible that between the cold air intake and the performance exhaust that I've overwhelmed the stock valves ability to move air in and exhaust out. I'm thinking that I may need to upgrade the heads and cam. Any thoughts?

Thanks again