Shopping for heads, I see some have raised exhaust ports and others do not. Does this mean my headers will sit a certain amount above the stock location? This could be a problem with Lightning Headers and Teague switchable tips as there is very little room between the two.

Most of the latest aftermarket heads are raised .600 over stock. The ones that aren't raised, unfortunately, are not the best performance wise. I think Edelbrock's marine roval as used on the 525 has stock location as does the Merlin oval and rect.

I just did a couple of sets of dart iron eagles
that are raised .300" that have CMI exhaust and
captains call, and had no alignment issues.

My Merlins where raised as well.

If you are talking big block chevy engines, when the exhaust ports are raised substantialy anywhere from .250 to .600, the exhaust flange mounting holes are drilled at standard heights relative to the exhaust port itself so any manifold or marine header should bolt up just fine and a quick check with the exhaust flange gasket should confirm that. The only real problems that could show up are overall manifold riser or header pipe overall height, especially on tall deck engines, where the height of these units might get to close to an engine hatch or cover, or on a boat where the exhaust captains call or tailpipe system is hard piped to and thru the transom which is some cases can go out of height alignment enough to prevent recoupling the pipes without using longer flexible rubber connection sections.

Best Regards,
Ray @ Raylar

You can usually get away with .300 without having a problem. Any more than that, it depends on how much play you have in the system to juggle it around. As Patriyacht said, the higher the port is raised, the better it will flow since the short side radius is not as tight. You may be able to go to the silicone hose instead of the black steel reinforced rubber since it will flex quite a bit more and it is more forgiving in tight bends. It's not cheap, but you should not need much.
Eddie