I tapped and installed allen plugs in the hot slots on both of my 67 396 Camaro's. I left the riser valve alone though. That opens fairly quick anyways and I don't see how that would contribute to performance issues. The stock exhaust manifolds are the large performance reduction culprits (you can work around that a little by using a cam with a slightly longer exhaust profile). I did install a restrictor in the intake manifold gasket crossover opening to limit the amount of flow under the intake mainly to reduce paint discoloration and flaking at the ends but still retaining the functionality of the choke coil.
If you intend to drive the car in cool weather or show the car I would recommend to leave the exhaust valve in place.
I don't think any of us use the cars today the way they were intended due to their antique status and value, including performance concerns, so aside from the hot slot plugs, I would recommend to leave the rest intact.