You guys are going to have Will twisted in knots before he even gets his Cobra ordered. And you aren't doing his budget any favors either. LOL ......
Will, trust your gut for a lot of these decisions, or you'll be going back and forth forever and never get your car. But keep in mind, some of these "specialty" paints can get very expensive. The paint alone for my Cobra was near $1,000 a gallon and that didn't include the labor, clear coat or stripe color. Some paints are much more expensive, depending on supplier, color, pearls and metals in them, etc....
As for engines, nothing cooler in a Cobra than an FE, but also the most expensive route to take. If you must have an FE and the budget is tight, try to find a used one that someone is changing over to something else for whatever reason. I've seen some real deals come up on FE engines that were extremely low mileage for various reasons guys were moving them along.
Is there a Cobra club in your area? If so, join in and attend a few meetings. Get to know the guys and their cars and start to really look at what you would like to build. It will be an eye opener for sure.....
Bob