One additional thought for your parts list: upgraded cooling system.
I would have to read back in your thread because I don't remember if you've already tackled that subject. But if not, you should consider upgrading the radiator at a minimum. With the added heat rejection of the new power level with the blower, the stock radiator probably isn't going to be up to the task.
Here's what I've been told by colleagues that worked at Ford (I'm not 100% on the info, but it came from reliable sources and I can throw in some personal experience as well): The '94/'95 V8s and V6s share the same radiator. It's on the big side for the V6 and acceptable for street-duty 5.0s, but borderline with built motors and no good at all for road racing or built motors in hot climates / hot summer days. I can confirm the road racing issue. I have to watch my temp gauge closely on track days hotter than mid 60s with a stock Cobra long-block. Also, '96 Cobras had a TSB of some sort where owners could get an improved cooling system (I think it was a just larger radiator) if they came in to dealers under warranty with cooling system complaints. I believe '97+ Cobras had the improved systems from the factory.
Great project and nice planning! I'm anxious to keep following this build and watch your progress.