I came from 3rd gen Camaro's so seems about the same, I am already seeing the cam phazers suck.
Welcome to the 3V Mustang brotherhood.
Your car is a good blank canvas for some tasteful mods. You many miles does it have on the odometer?. You said it's a Deluxe model and that came from the factory with cloth seats, so a previous owner must have swapped in a set of red leather seats (which look nice by the way) from a Premium model.
The first thing I'd advise you to do, after you've installed a pair of mufflers, is to have the ECU scanned for fault codes. This will identify the source of the misfire. It could well be the spark plugs if they've never been changed since the car was new. In that case beware 'cause they can break when you try to extract them and have a Lisle tool handy.
The cam phasers can fail prematurely if the engine's frequently revved hard, or if the engine oil isn't changed regularly causing the VCT solenoids to clog up and starve the phasers of oil, but normally they'd be expected to last at least 150k miles like the rest of the timing system (chains, guides, tensioners).
Sixteen year old cars will come with teenage problems if previous owners didn't keep up with preventive maintenance, so be prepared to fix a few things first before you start modding (unless the mod is an upgrade and a fix at the same time). When you get the opportunity, raise the car on a lift and perform a thorough underbody inspection for possible damage, fluid leaks, and wear in suspension components (especially bushings).