Ongoing Coyote Problem

[tims210]

I'm at my wits end trying to resolve an issue that's been ongoing since last season. To start, I have a gen 1 motor with 3000 miles on it. I'm experiencing fluctuating hesitation upon hard throttle. It's not a linear hesitation. It's more like a sputtering hesitation. I also have sporadic pop coming from the exhaust at idle. Not a backfire but an intermittent spit/pop kind of sound. The exhaust isn't blowing any smoke. I also have knocking at lower RPM's under normal throttle. My gas is fresh with the correct grade. I changed the mass airflow sensor and no luck. I looked for vacuum leaks but I can't find one unless I overlooked something. I pulled the spark plugs and they look normal to me. My dealer was very gracious in giving guidance. I was told to data log my car using SCT Live Link. I have the Lund tune by the way. He was concerned about the following variable valve timing readings.

VVT exhaust bank 1: actual value -.12 min value-3.37 max value 31 Avg 7.0
VVT exhaust bank 2: actual value -.12 min value -1.4 max value 31 Avg 7.0
VVT intake bank 1: actual value 0.0 min value -47 max value 1.25 Avg -5.5
VVT intake bank 2: actual value .07 min value -47 max value 1.3 Avg -5.6

These numbers were logged going no more than 4500 RPM since the problem worried me. I backed off to prevent any possible damage. He claims the banks shouldn't read this far apart from each other. Should only be a percent or two.The knocking is also reading on the log results, but the engine is adjusting timing to compensate. The fuel trim numbers looked good since the engine wasn't calling for more fuel. We pretty much ruled out a clogged filter or pump issue. I don't understand why it's knocking in the first place. It's quite audible. I checked for any parts rattling against the engine to rule out false knocking. The only things I found were the chrome metal coil covers and hood prop rod. The covers did rattle so I put a small bead of RTV sealant under the corners and it stopped it. The prop rod was rattling against the metal oil fill cap. I wrapped some thin foam around it and it fixed it. I plugged an OBD reader into the port and got no fault codes. I'm not sure if my problem has something to do with an electrical issue. I hope this doesn't have to do with a VCT solenoid. I don't know how I'm going to get the valve covers off given the very little room between them and the fender well.

Any guidance is much appreciated. Thanks.