Constant Voltage Regulator is bad. I get this call all the time (I work at one of the leader Mustang Parts retail stores). I'd put money on it being the CVR.
3500 seems steep for a car that needs that much work. I bought my 97 GT with Patriot stage 2, long tubes, gears, etc etc etc (tons of things done, even an ipod radio) for 5k.....
541 seems kind of inflated to me....9:1 at 10psi with a T-trim....is there something I'm not seeing here? Maybe I'm just stupid. What kind of dyno was it? Dynojet?
Welcome to my world! Being in the business it's extremely frusterating when a company is out of stock on an item and your customer is calling and yelling at you for not sending it out! These places do run out of stock on items