Yes, I have a 347 in my SN right now. I can give you all kinds of details.
First off, hood clearance. It's not the intake that gets you, it's the valve covers. Almost all stroker engines have roller rockers. That's like the standard. You can get pedastal mount rockers that will fit under stock Cobra valve covers. If you have stud mount rockers, like most stroker engines, things get more complicated. When I first put my stroker in, I had to put bigger valve covers on, which meant I had to add a phenolic spacer to the intake, which meant a taller hood. I later learned about Trick Flow valve covers.
Buy this valve cover.
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You have to drill your own hole for a oil fill tube, but it's worth it. I got these valve covers to clear stud mount rockers with no problems. No spacer. I had to grind a little metal on the bottom of the plenum of my Holley Systemax intake to work with the valve covers, but it was not a big issue. Always check your clearances with a certified quality clearance compound.
Almost everything bolts right up. The Cobra intake is a great intake. Using an SN Cobra intake is a great idea, because it makes bolting things up (like the EGR) that much simpler. I had TMoss port one for our Cobra car. He advertises 250cfm, which is more than most aftermarket heads flow. I can't speak highly enough about TMoss and the way he conducts his business. That intake will definitely clear the Trick Flow valve covers with the stock hood no problem. If you intend to keep a strut tower brace, you will need to get an aftermarket one. That stock GT one will not clear a Cobra intake.
Which direction do you want to go with your exhaust? I am currently running
BBK Foxbody 1 3/4" primary headers on my SN. There are some complications to that.
Do you want a cold air kit for the MAF? I have managed to get a 75mm MAF into the stock air box with some cutting. Runs great.
Kurt