This is my area of expertise. America's Tire MUST replace the lugnut and stud if they f*cked up. It's about a 15 minute job and costs them less than $10. Make damn sure you go back there and have them fix their screw-up. They should be more than happy to do so in order to save face.

On a different note, you don't want to remove the intake resonator. It swirls the intake charge, essentially forcing more air into the engine. You can do it if you want more sound, but I'd reccomend saving up for exhaust.