vnmous, if I were you I would work on the heads first, then the intake manifold. If your budget allows, do both. If not, you can always do the manifold later. You don't have to fully port the heads. Even just a multi-angle valve job along with blending the valve pockets and matching the intake port to a stock gasket would help significantly. It wouldn't be a "might pick you up" proposition. You would definitely feel the difference in the seat of your pants. This work can be done pretty quickly by a local performance machine shop. It usually only takes a few days. All you would need to do is shop around for the right machine shop and schedule some time with them so that your stuff gets worked on as soon as you drop it off. That way your car is not down long.
The valve job and bowl blend will pick up air flow on both the intake and the exhaust ports. But the intake ports gets the added gain of better air/fuel mixture quality. This is due to removing sharp edges and abrupt flow direction changes that cause air/fuel seperation. So in essence you'd be increasing flow quantity AND improving mixture quality at the same time.
It makes no sense to port the manifold without doing the heads, and it could even hurt flow and power if the manifold is opened up larger than the intake port on the head. This would be the case if you matched the manifold to the intake gasket, but did not do the same thing to the heads. This would allow any part of the intake flange of the head that is inside the gasket line to protrude into the flow path, causing turbulence, which hurts flow and power.