I have not done rear engine seal or a pan gasket on a Cobra/GT. But to do the rear engine seal you need to pull the trans, clutch, and flywheel to gain access to the seal. There may be a special tool to install it. When I worked on trucks Mack has a special tool to install the seal. Without that tool, it is guaranteed to leak every time.
I am not saying Ford is the same way. I am just putting it out there so you can do your research before you have to do it twice.
The oil pan gasket you will either have to drop the k-member or pull the engine to get the pan off.
Both are allot of work. Neither will be fun.
Good luck.