Well you did say that you have never driven a mustang before and that probably made a bigger difference than anything else.Other than that the other guys have some good ideas but also since you bought this car modified you have no idea of what kind of shape the tune is in or what else or lack there of was upgraded.
The car is most probably running too rich (Im asumingthe previous owner was smart enough to upgrade the fuel system other than just an adj regulator and people tend to get to carried away with jacking up the fuel pressure anyway) but speaking of the regulator what is your fuel pressure set at? you do have boost and fuel pressure gauges right?
Leaving the stock headers would be a bad move but adding the off road pipe and cat back kit would be a good idea.
Given that the air filter was that dirty the previous owner may have let many other things with the car lapse so the best thing you can do is have the car run on a chassis dyno and data log it to really see what kind of condition (not to mention how much power its making) the car is in.Just throwing on a blower does not a fast car make-trust me I know
Oh yeah,3:55 gears are a great all-around gear choice and if your gears are stock I would bet there are probably 3:08's.
J.