I added a little boost to old my 95GTS with the Cobra intake, GT-40Y heads, cam, exhaust, etc. Originally, I ran only 6lbs of boost with 24lb injectors, a 155lph intank fuel pump, 6:1 fmu, and a custom dyno-tune by Danny Swanson. The car never had a hiccup and ran like a champ, making 380rwhp/367rwtq. I later upped the boost with a larger crank pulley and powerpipe, added 30# injectors, a 255lph fuel pump, changed to a 4:1 fmu, and had it dyno-tuned once again. I never drove the car hard after making any boost/fuel changes without tuning it first. Again, the car ran awesome with these basic upgrades. The air-fuel was safe and I never ran into any problems until I got greedy with the boost. Keep it at 6-8psi with the mods ss93cobra said and you should be good to go.
For a better Cobra example, I know two guys who ran a mild amount of boost on a well tuned engine for many miles. One of them ran 6lbs of boost on his 94 Cobra without issue for over 50,000 miles. The other guy was a member of a mustang club I used to belong to. He was approaching 147,000 miles apparently around 100,000 of those with boost. He never went more than 8psi and as his engine increased in miles, he usually had his car detuned a bit.