Dude I totally feel where you are coming from. I'm not looking for huge power, actually. I realistically only want 400-500 wheel.
One of my friends runs a 1998 GT with the 2V and a rear-mount turbo, he's very knowledgable about Mustang things. He confirmed my suspicion that for moderate power the 3V is actually the way to go, and is where I'm headed.
I will need the E-brake but I can convert in the long or short run to hydraulic. Worst-case scenario I can relocate the E-brake gizzards inside the cabin to gain clearance.
$10k worth of stuff (not including chassis) is about what I am thinking, but it will realistically end up being, as you say, between $15-20. This project will probably evolve over the course of the year in many different steps. I have some capability myself and with friends and associates to fabricate and wire, but I'm trying to keep that to a relative minimum.
That's why I am trying to stick with the Ford ECM and management for the 3V, if possible. LS1 ECM and management is already basically standalone and you can purchase harnesses that essentially make it so. I am hoping that there is good programmable support for the Ford ECM so that I can go that route, otherwise I will probably go MegaSquirt. FI is not in the plans for the first go-around. Factory gauges and electronic diddles were planned to be nixed before the project started -- no need for ABS, TC, AC, etc. All I will keep inside the dash is the HVAC blower which will be plumbed fixed up to windshield (defrost) and through my helmet (ghetto-rigged cold air).
I don't plan on this getting done soon as it is not looking like I will have a title sponsor for 2008. If I have the chassis, motor, suspension, and diff by the spring, I will be delighted.
Please keep us all posted on the progress of your differential build -- I might want to get one of those front x-members for the diff from you.