Blain,
I don't have positive news for you. The 530 we are building is using the Edelbrock heads which have stock valve cover rails. We were using the Crane Gold race roller rockers and at full lift (.650), they lifted the valve covers off the block and gasket about 1/16-3/8". So, they would need a double thick gasket to clear. Unlike the small blocks which have these available, I am not aware of any for the 460's. You would have to glue a pair of std gaskets together, and use valve cover studs. This can be done, but the gaskets do not hold up as long as stock ones(they tend to seep more) - not much of an issue on a typical Cobra as they don't see thousands of miles a year.
The rockers only hit the baffle at each end of the head. The baffle really should not be modified, as it is already designed to fit very tightly against the inside of the cover, and removal would result in a valve cover that is always leaking
oil out the
oil fill/breather holes. On our engine, we had already planned on using the spacers and didn't have a problem, but they will put you well over your 4" max height.
Now, one other question is which heads you are running. The Blue Thunder 460 heads are designed with 3/8" taller valve cover rails, which would allow for the clearance needed, while the other stock and aftermarket heads are std height and too short.
Hope I have helped a little. Let me know if you have some more questions.
Rob