OK I can dig that trade big time.
A few questions and pointers. Is the connection for the intake breather just open?

That would cause all kinds of issues. I would pull off that little filter and put the pipe back on on the passenger head. Also on the drivers side head you should put a Steeda oil catcher/filter as it will save the heat exchanger from getting covered in oil.
The 03 tick and 04s not having it is a myth. Lots of BS floated around for a long time about that and really the heads are identical. The big BS statement was if it has a blue stripe then it was the revised head.

Same head. The dreded tick is caused by WOT runs in the upper gears and there being noplace for the coolant to go on the back of the drivers side head. The mod for that used to be a major PITA but now Evenflow had the kit that hooks up on the top of the head. That will get rid of having the potential head tick problem.
Was the fuel system upgraded to Cobra spec? Dual pumps with the baffled tank?
If you want more HP then its gonna cost some money. 470 ish is the peak of efficency for the Eaton. Even ported when you push 500 out of it then its just a real bad heat pump and needs to be rebuilt every 10K miles. Sell the Heaton and get a Whipple or KB and make 100 more HP at the same boost level. Also get the dual FPDM and that allows the pumps to run better and cooler thus supplying more fuel. If you have the stock MAF then ditch it and get a new one. The stocker pegs at 450+ rwhp.
As to looks, I really dig it but some simple mods will make a world of difference. Add a Mach 1 spoiler up front, Mach1 grill delete and a set of 03/04 Terminater headlights. They are smoked instead of chrome and look way better. Also ditch the GT side skirts and replace them with 03/04 Cobra versions. You will be amazed how much wider the car appears with them.
If you have any questions please feel free to ask. I know the SN cars very well and 03/04 Cobras like the back of my hand ..... *looks at hand* where did that mole come from?