Late model Junkyard parts for 66 restoration

Contrary to popular belief, I was driving those cars when they were new, and they are safe just the way they came out of the factory. However there are a couple of things they have done over the years to improve them greatly.
#1) While drum brakes were fine stopping on a nice day, the major drawback was water, they tend to fail when wet. So changing the fronts to power disc is a major improvement. If I were to do that I would likely go with 5 lug, which means a rear end swap as well, but you can use an 8", 8.8", or 9", they are all good differentials. I like the 9" because they are easy to work on, and quick to swap gears. And personally I've acquired a collection of them over the years.
#2) Radial tires are a huge improvement in handling, braking and wear. And if you go with radials you need to add a panard bar to the rear to keep the axle from roaming on hard turns.
#3) If I were keeping the 6 cylinder, I would keep it manual steering, the stock power steering in the early mustangs leaves a lot to be desired. I'm used to it so I like it but most people after coming out of a rack and pinion car have a problem getting used to the free play. I still have manual steering in my CJ and like it. If you need to go with power you'll either have to go to a rack and pinion, or stick with the stock power steering and get used to the way it drives. There is absolutely nothing unsafe about the stock power steering, you just need to get used to the way it feels.

That should make the car a nice daily driver, after that there is a host of little things like intermittent wipers, cruise control, a nice stereo that you will probably miss when you start driving a classic. But they can be added at any time after you're using the car.