Anyone know what could be causing this between 5-5500 rpms?

 

I'd say likely wires or plugs. But also this happens on LS1's with some dyno operators who can't get good grounds when dynoing.

 

I have the same problem. My dyno sheet actually looks much worse(the dips and are worse, its pretty jagged). I think mine is ignition related, but I haven't sorted it out yet. I will be doing a heads/cam installation this coming weekend so I will just replace the opti and coil and hope that it cures it. I would check the plugs and wires first since that would be the easiest place to start.

 

The plugs are less than 1000 miles old, and I know it didn't do it on atleast one of the runs.

 

Knock retard maybe?