[TJ]

You have a lot to consider with this project. The dropped axle is the best way to go on the front. You will have to bend the steering arms to get the correct turning radius when using the axle. The alternative is to cut off the arms and use some bolt on steeriing arms.
The parallel leaf kit in the rear will lower the car and gives more rear stability. The later Ford rear is easy to work on and you have less chance of breaking an axle. If you use the late rear you will have to use an open drive transmission with the flathead. You can use the trans from a 42-50 Ford pickup. An alternative is to put a C-4 automatic behind the flathead.
If you stick with the stock rear end you can de-arch the rear spring to get it lower or buy a lower spring from one of the rod shops. Whatever you do set your plan and stick with it. Changing ideas in midstream usually costs a lot more money.
If you go the route of a later rear end you can use the 67-70 Mustang or the Maverick rear. The Maverick is narrower than the Mustang, so you will have to be careful of the offset of the rear wheels. Either rear will work with the spring kit without moving the spring pads. You will have to slightly egg shape the hole in the pad to get it to snap over the spring center bolt. I've done several of these conversions and prefer the 67-70 Mustang rear.