So Stotzbotz,
Seems to me that if you have the right intake gaskets, and if the intake to head to valley interface is correct (block decked or heads milled requires adjustment of the intake mating surfaces, or the "china wall" for proper spacing) you'd be better off leaving the crossover ports functional, to improve cold/cool weather driveability, and quicker warmups in cold weather. Now given your Tallahassee location you may not be concerned with cool weather, but I'd still consider leaving the passages functional. There's no reason for your smoke to be due to those ports if your gaskets are sealing right.