Engine 1991 Fox body runs like crap with hood closed

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There is a fat wire harness that goes over each strut tower. Perhaps your hood is disturbing one of those harnesses and causing an electrical issue? Maybe shake, wiggle, and push down each harness while running and the hood open and see if anything becomes ovious?
Also lower the hood slow with engine running as you peek underneath and see if it’s hitting anything. Maybe touching the battery terminal(s)?
This might sound dumb but if you have an aftermarket alarm with one of those switches that reads the hood open/closed maybe check that switch if it’s faulty and causing an issue.

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Do you have an open air filter element and an exhaust leak? If so it could be the carbon monoxide that is choking it.

When I first got my jet boat, the water log headers leaked exhaust a bit, I didn't think anything about it but after about 15-20 min out on the water the thing would start running bad and have no power. Id open the engine cover and it would run normal. Then after another 15 min, it would do it again. After a couple beers at the camp fire that night, it dawned on me that the thing was choking itself out from the carbon monoxide. I wedged a couple small 2x4's to keep the engine compartment slightly open. That gave the engine enough fresh air that it ran great the rest of that trip. Then I fixed the exhaust leak when I got home.
 
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