since i have my engine out would it be worth the timeport matching my heads and lower intake to a bigger fel pro gasket? could i see any gains from it?
Doubtful they'd be significant - and some folks find that opening up one that far can hurt low speed flow velocity/torque. Port matching is fine on a blueprinted engine for tight rules/class racing where every single HP matters. Unless that's what the engine is for, I don't think it's worth the trouble - unless of course you just want to do it.
I agree with Michael about the gains from just increasing the size. What you should concentrate your efforts on is making sure the ports you already have line up. By carefully positioning the intake on the heads and making sure that there is no mismatch. It is sometimes nessecary to remove small amounts of material or milling the intake in order to achieve a perfect match, but without removing more material than is needed.
The most I would do is match the intake to the heads - make your own templates from the heads and lay them on the intake. Leave the intake runners .020" or so smaller than the head runner for alignment to avoid a mismatch.