I know this is the hardest option, but I say wait until the '06 Cobra comes out. It should blow the '03's off the road and even if it doesn't it will definitely drive their prices down. In the meantime keep the cars you have and just quit modding them. I know it is hard to do believe me! (I am trying to do the same thing)
I had a GT I wanted to put a blower on, build a motor for and work over, but I don't have facilities and the time to do most of the work. I also can't be without my car for an extended period of time. I traded my 02 GT and got the 03 Cobra. I only paid $28,500 for the Cobra after my trade. That made it affordable for me. Now I have a 400+HP Daily driver that rides nice and has kick arse seats for those long trips home on the weekends. I'd also have to disagree with tait_gt2002 on the tranny. 5th on the T56 is great. It lets you have another option in your power band up top. 6th also is a great overdrive gear. The tranny ratio is only slightly lower at 0.63 compared to the 0.62 in the 3650 GT tranny. The 3.55 rear end makes the rpms a little higher on the interstate than a stock GT with a 3.27, but it works well and gets over 20mpg. I'm happy with it.
You already have a good 550HP Daily Driver. You could mess with the GT and make it pretty nasty too. 550HP through AWD probably wouldn't be too bad on a rainy day.
Actually the tire isn't flat, but the car is out of alignment due to some suspension work, done when the engine got reinstalled. So the wheel camber is way off right now, I plan on finishing the clear this weekend then taking it in to the alignment shop next week. Then I can drive it again, if I want to...it eats premium gas though and it costly to fill up these days. But it does get 25mpg. I have to break the new motor in before I sell it anyway. 500 miles.
I agree, there is way too much crap on the hood of the 69, but it is in primer awaiting its turn. Stealth paint is almost done, then I get to start on the charger paint, but still have some chrome to remove first. That big flat surface is just too convenient.
Either car is nice, but if you ever want over 450rwhp go with the cobra. I think you'd sacrifice way too much money to make the GT go higher reliably. The cobra is a higher starting point in handling and hp potential.
The cobra also wakes up at 2400 rpm stock. It's a nice feeling.