First off, you MUST set your base timing with the diag port terminals shorted, or you effectively have no idea of your base timing.

Start by setting your base timing to 5 degrees with the terminals shorted.  Also, double check your TPS settings to be sure you're IDL contacts are working properly.  If you don't have that set properly, your idle and everything will be screwy.

I experienced a miss in my engine at about 2000 RPM cruising under light throttle- it turned out to be my timing was too far advanced.  I ended up running mine at about 7 degrees, and I always run premium fuel.  My engine has a TRD Stage II cam, TRD Header, and a gasket matched intake.  I also polished the intake runners and had the injectors balanced.  Depending on your altitude, you may be able to advance the timing more than that.

Ryan