I'm having a similar issue with my 2006 4.6L. It starts and runs okay, until I try to accelerate quickly. Then it does mild missing, and bogs down. My scan tool showed a pending fault on cylinder 3, and I replaced the coil. I already had the plugs changed at 183,00 and we are at 186,000. I took it back to the dealer who installed the plugs, and they did a diagnosis. 3 plugs needed to be replaced and they wanted to replace a valve cover because the screw holes for some coil packs were becoming compromised. To summarize, they wanted $1,400, with no guarantees that the missing would be addressed. The car was running lean, and they would try to find out why, after the $1,400 robbery without a weapon. I ordered the parts and will do the repair. All the sensors are good, so I'm leaning to something mechanical as the cause for my issue. Any thoughts or suggestions?