Great start to a new adventure!
Like you, I am also new to The Club. I wasn't brave enough or wise enough to attempt the build. So I purchased a completed vehicle directly from Backdraft in Boynton Beach.
It has the Gen 3 Coyote and a Tremec TKO 600 5-speed. I am very happy with the engine /trans choice. Although it still has some tuning issues. My setup is a 2018 Ford Performance crate engine (P/N M-6017-A50C) and utilizes the Ford Performance control pack (P/N M-6017-M50B).
I am sure some more knowledgable members may correct me. But using a junkyard Gen 3 Coyote may present some interesting problems regarding the PCM. Late model Coyote PCMs are locked to the VIN by way of the Body Control Module. It may be necessary for you to purchase the new Control Pack.
The composite
oil pan will probably be a problem. Moroso makes a pan specifically for Cobra kit cars with 5.0L installs (Moroso P/N 20570). I have also read of clearance problems with the alternator due to the tight fit.
Enjoy the adventure. I sure both of us will learn a lot by reading this thread