easyist way to chech and make sure what cyl is missing is to pull coils from plugs when running if you pull coil and does not effect running is cyl missing just because coil tested ok doesn't really guarantee ok they go out when hot may test ok cold you could try spraying brake clean or carb cleaner to check for vac leak once determine which cyl missing you can swap coils with other cyl see if miss moves, if doesn't is not spark concern pos injector concern
if intake was cracked you would think something would show up when spraying with carb cleaner and would not cause low compression would still be pulling air into cyl
if you had injector sticking could wash down cyl poss cause slightly low comp are plugs on missing cyl wet could be valve concern /carbon built up on valve have seen that
may not make sense but if you remove check valve from comp guage hose and take eng running compression needle will fluicate if needle stops moving at times could be valve sticking compression is built in cyl should build comp even if intake is off because it is still pulling air in
i once had older crown civ with bottom of intake blown off and vech still ran crappy but ran could hardly believe it
A problem with intake would NOT cause low compression. You must have proper compression before proceeding [you already said you have low compression on #7 and a misfire on that cylinder] What are the compression readings?
Ignore it running correctly cold, this would be do to the pcm increasing fuel pulse width [more fuel] during warm up.
A cylinder leakage test would be the next diagnostic step to determine if its valve train or rings. Also do a wet compression test. Pull the valve cover and inspect the rockers for a problem on #7