Bolts 7 and 8 are the ones I'm having difficulty with. I just installed new valve covers, spark plugs, and coil packs. Which is why I had the lower plenum apart. It's possible they weren't even on in the first place as I only had those 6 middle bolts and I'm not seeing 2 M6 bolts that should of been along with those middle bolts. The intake manifold gasket is preventing any access to those two outside holes. Everything else is in place and I had no issues with the middle bolts. There isn't any other way to set this gasket, I've read somewhere that this gasket isn't even necessary. But I'm not too inclined to believe this. I went ahead and used RTV to help create a better seal on the outside of this gasket. But if because these 2 bolts are missing,is it possible I'd have a leak anyways due to it not being torqued down enough onto the intake Manifold? Maybe I should go back and take everything apart. Should I of just cut the two ends of the gasket so it's no longer blocking those holes? Guess I'll just go ahead and see if I have any issue pop up. I'm almost done, I just need to reposition where I'm going to put the oil catch can at. I went ahead and put in a pcv delete. There wasn't any oil pooling up in the runners, it was dirty and there were traces of oil but nothing bad. It is however burning a lot of oil, I'm having to put in about half a quart of oil every 500 miles give or take. The catch can is probably not even needed. Anyways has anyone had this issue with the intake manifold gasket preventing access for the outside bolts? I can't seem to find any examples of this happening to anyone else before.

 

With further research I noticed that there's supposed to be two studs on the two ends of the upper intake manifold. The gasket can be seated in place by these studs, helping to keep it in place during install. I don't have these studs at all, so I knew that I wasn't tripping when I couldn't recall ever removing a bolt or nut from that spot. Apparently it never had an issue if these studs have been missing. No telling how long it has been this way too. I just find it odd that there isn't any studs here, when it's obviously supposed to be there. I don't know why they were even removed. I was thinking the whole time that it was supposed to be a bolt.
Only thing that could of happened was that they somehow came off when I removed the lower plenum. This is a worse case nightmare scenerio here. Especially if they somehow fell down into the intake. But I'm positive this isn't the case, I would of definitely noticed that. Since I don't even recall removing any nuts there in the first place. But it does have me a bit concerned. Maybe I should take everything apart to be certain. But I don't even have a way to look down in there. Those studs shouldn't of been that loose to just fall off so easily. They were either removed for some reason, or they were never on there in the first place. Seems really odd to me though, hopefully everything will be ok.

 

Maybe the stud came out with the nut when it was removed???
When I installed the motordyne 5/16" spacer, you have to remove the 2 studs from the lower plenum (studs are too short when you add the plenum spacer). Mine came out quite easily with two nuts tightened together (!).

 

I think you are confusing what I was attempting to describe for the studs on the plenum. I was talking about the studs that go on the outside of the Intake Manifold. It's #7&8 on the diagrams, they are on the outside. One close to the firewall with the other being in the opposite side towards the front of the engine. You can see them whenever you look down underneath the plenum. You have the 6 bolts that bolt down the lower plenum onto the upper intake manifold. They bolt together and hold the intake manifold gasket down. I'm not sure how both studs were broken off. I did find a broken stud that has the nut still on it. Not sure if this came from my car or my brothers. But I'm thinking it may of cane from mine. It had me worried honestly that the other one somehow fell into the intake on top of the valves. I don't even recall ever having to take off any nuts when I removed the lower plenum from the intake. So far, so good though as I don't have any vacuum leaks. I have no cel, only thing I have is a low idle at times whenever it's warmed up and the car is just sitting at idle. It'll feel like it wants to bog out and die,but it never does. The idle sits around 550-650 rpm, it was running lean at first because of the plenum spacer. I had A/F codes at first so I took out the plugs on the bank 2 side to clean them. Because they were wet and dark from running lean. Plus I accidentally had cylinder 4&6 swapped on the coils. That caused a misfire, so those plugs needed cleaned. I fixed that issue and then somehow had a connection on the bank 1 side disconnect causing another code for the A/F sensor. After I fixed all of that, it was still running lean because I had a vacuum leak going to the oil catch can. All issues have been fixed and it's running great so far.