Is the valve cover hitting the intake runners? Its a pretty common problem with aftermarket intakes and valve cover combo's. I had to grind the crap out of my intake runners, and install 3/8" spacers to fit my Edelbrock valve covers to my Weiand intake with SpeedMaster Heads. There is a guy who sells spacers on ebay and Moroso sells a steel core silicone reusable gasket that is 3/16" thick that seals well.
GASKET, VALVE COVER, SMALL BLOCK MOPAR
Also are you running a PCV valve on one valve cover and a vent tube to the air cleaner on the other?