should be fine on the O-ring then. If its soft it will seal. After decades they get hard as a rock and will shatter if you poke at them. Same with the PCV valve grommet. I've actually stood on them without it deforming before, and I'm something of a fat ass.
oil on the alternator bolt probably wicked there from a leaky valve cover gasket. Those go into a blind hole in the head. If the valve cover gaskets aren't the rubber ones, I'd change them while you have it open. Cork just don't last forever. Otherwise no need to open it. If the engine is nasty inside, you'll see it from inside the lifter galley when the lower intake comes off.
Make sure the gasket surfaces are clean and flat. If there is pitting, a very very light wipe of RTV around the coolant passages will work. You want a dab in the 4 corners where the side gaskets meet the end wall gaskets. I use long bolts with the heads cut off as guide pins to hold the gaskets and align the intake on assembly. Pretty sure its a 5/16" bolt. If you get four that are 4" long and chop the heads off that'll do it.
A few random suggestions. If you're removing the injectors from the lower intake, replace the O rings on them. If the caps are cracked you can get those too. Sometimes its sold as an "injector rebuild kit", but it will come with the cap and a pair of O rings. Might also not be a terrible idea to replace the fuel rail O rings either. You want the Viton seals. Not sure if the parts stores have them but its the same O rings Mustangs use, and I've bought them from Mustang places before. Usually they recycle OK but I have torn them in the past. I'd also give the upper and lower intake a good cleaning inside and out. The goo and sludge in there won't be doing you any performance favors. Don't get crazy trying to get it pristine but if you've got a big tote that you can mix up some degreaser in to let it soak, may as well. The Duplicolor Cast Coat Alumimum does a nice job of making things look like fresh raw cast aluminum too if you have any desire to pretty it up. The upper intake was painted a grey color but the lower was just raw aluminum.
oil on the alternator bolt probably wicked there from a leaky valve cover gasket. Those go into a blind hole in the head. If the valve cover gaskets aren't the rubber ones, I'd change them while you have it open. Cork just don't last forever. Otherwise no need to open it. If the engine is nasty inside, you'll see it from inside the lifter galley when the lower intake comes off.
Make sure the gasket surfaces are clean and flat. If there is pitting, a very very light wipe of RTV around the coolant passages will work. You want a dab in the 4 corners where the side gaskets meet the end wall gaskets. I use long bolts with the heads cut off as guide pins to hold the gaskets and align the intake on assembly. Pretty sure its a 5/16" bolt. If you get four that are 4" long and chop the heads off that'll do it.
A few random suggestions. If you're removing the injectors from the lower intake, replace the O rings on them. If the caps are cracked you can get those too. Sometimes its sold as an "injector rebuild kit", but it will come with the cap and a pair of O rings. Might also not be a terrible idea to replace the fuel rail O rings either. You want the Viton seals. Not sure if the parts stores have them but its the same O rings Mustangs use, and I've bought them from Mustang places before. Usually they recycle OK but I have torn them in the past. I'd also give the upper and lower intake a good cleaning inside and out. The goo and sludge in there won't be doing you any performance favors. Don't get crazy trying to get it pristine but if you've got a big tote that you can mix up some degreaser in to let it soak, may as well. The Duplicolor Cast Coat Alumimum does a nice job of making things look like fresh raw cast aluminum too if you have any desire to pretty it up. The upper intake was painted a grey color but the lower was just raw aluminum.
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