Just for clarification...you don't have any coolant lines hooked up to the intake?? I know the Cobra intakes have the EGR system built into them, but you should have coolant lines going to the EGR system on the intake to cool the recycled exhaust gasses. Maybe I just read your reply wrong or misunderstood you.
If you're not running the coolant lines to the EGR system, that's why it got so hot right there. Maybe the previous owner eliminated all the emissions systems and didn't run the EGR, so he never had the coolant lines run. So if you hooked it up without coolant, it gets plenty warm.
Then again, I don't know jack about Cobra intakes, so maybe I'm just all confused.
--nathan
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'91 GT, Coast 347, 9.5:1 compression, full intake, Wolverine 1087 cam, exhaust, Keith Craft ported Windsor Jr. Irons (235 cfm intake, 195 cfm exhaust), AOD, PI 3500 converter, Lentech valve body, 3.73's (4.10's in the works), and Yokohama ES100's out back.
Daily Car: '04 Infiniti G35 Sedan 6MT