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“For example if the VP is dead and President in a coma, can section 4 of the 25th even be invoked (without the VP)? Would the only recourse be to impeach and remove the comatose President? Or does the succession act have a provision for that?”
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Article II says, inter alia, that the VP shall act as President in the case of “inability to discharge the powers” by the President, and empowers Congress to legislate as to who would act as President if neither the President and VP can discharge such powers. Such language would seem to give Congress leeway to declare a President to be disabled, which, of course, would be very dangerous and one of the reasons why Congress proposed the 25th Amendment. Given that the 25th Amendment came later and is more specific as to how a President’s “inability” is declared, I don’t think that Congress may rely on Article II to declare a President to be unable to discharge the powers of the office and instead the process set forth in the 25th Amendment must play itself out. Since Section 4 of the 25th Amendment provides that the VP (along with a majority of Cabinet officers) has to sign on to any inability certification before it may be presented to Congress, some wooden literalist may claim that if there is a vacancy in the Vice Presidency then the President never can be declared unable. However, the most reasonable reading of Section 4 is that the VP must sign on *if there is a VP*, and otherwise a majority of Cabinet officers (or of such other body that Congress designates by legislation) would suffice. Things not covered by the 25th Amendment would be filled in by Congress, since Article II still applies except where specifically preempted by the 25th Amendment. So if a majority of Cabinet officers declare the President unable, and there is a vacancy in the Vice Presidency, the holder of the office next in line in the line-of-succession law would become Acting President. Of course, pursuant to Section 4, the President would get his power back if he communicated to Congress that he was able to exercise his powers, unless a majority of the Cabinet again claimed that he was unable, in which case Congress would decide the issue (with a 2/3 vote from each house required in order to declare the President unable).

Of course, had the President nominated a VP prior to going into the coma or whatever it was that happened to him, then Congress could confirm his VP nominee and then there would be a VP that could participate in the Section 4 process, and the issue of how to treat a vacancy in the Vice Presidency would be moot.

But what if there was no vacancy in the VP, but the VP was in a coma or something? That would be much murkier ground, since the 25th Amendment is silent on the subject of VP inability and Article II empowers Congress to legislate as to who would act as President in both the President and VP were unable, but not to declare the VP to be unable *in the absence of having the inability being needed to declare another officer to be Acting President*. That would create a quandary, but I think that ultimately the certification from a majority of Cabinet officers as to the President’s inability would be deemed sufficient if the VP was assumed to be disabled unless the VP objected to being deemed to be disabled (and, of course, objected to the President being declared unable).

“To clarify if there is a permanent vacancy and someone below VP takes over they are they the President? That would make sense but the succession act seems to say they’d still only be Acting President.”
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The language of Article II (and of the line-of-succession law) speak of who will act as President, and in the case of temporary vacancies that is exactly what occurs. However, only a VP that becomes President truly can be said to be filling a permanent vacancy.

If, say, the Secretary of the Treasury is next in line to act as President due to the death of the President and VP and vacancies in the offices above the Secretary of the Treasury in the line-of-succession law, the Secretary of the Treasury would be the Acting President, but not the President properly speaking, because he would serve not until the next election, but until an office higher than his in the line of succession was filled. For example, if the Secretary of the Treasury acting as President were to nominate a Secretary of State, and such nominee was confirmed by the Senate, then the new Secretary of State would become Acting President. (I’m not including hypotheticals involving the Speaker of the House or the President pro tempore of the Senate given that I don’t believe that such persons constitutionally may be in the line of succession.)

And even if there was a permanent vacancy in the Presidency and the Vice Presidency and the first person in the line of succession (say, the Secretary of State) was the Acting President, it still would not result in such person being the President proper, given that (i) such Acting President could nominate someone else to serve as Secretary of State, and upon confirmation such new Secretary of State would become Acting President and (ii) Congress has the constitutional power to amend the line-of-succession law so that the Secretary of State no longer is first in line, which would make a different officer the new Acting President. While such actions are unlikely (and the latter certainly could be questioned in court), they certainly are possible, and thus an officer other than the VP will be a mere Acting President no matter what happens. Happily, this is consistent with the language of Article II that authorizes Congress to legislate as to which Officer shall “act” as President.

Please note that some scholars believe that Congress could call a new presidential election if both the President and VP die, but I’m not touching that one with a ten-foot pole. : )