Good morning, good afternoon, good evening, and good night.

After about 30 minutes on a crash course of learning about Genders of german, I finally have this straightened out.

Why is there a difference in "gut" (good) when concerning the phrases, "guten morgen" and "gute nacht" or good morning, and good nigh, respectively?

Well, it has to do with genders. German, like spanish has genders. Although German has three.

Masculine: Der-- as in, der Morgen.
Neutral: Das-- as in Das Auto.
Feminine: Die-- as in Die Nacht.

As such, Morgen is masculine. It should be Guder; however, in the case of the phrase "good morning", it falls into the accusative case. For some reason in the accusitive case, the masculine form of a word changes from ER to EN. This is why good morning is "guten morgen.
This is also the gase with "good evening", and "good day". Evening and day are masculine, and would be "der abend" and "der tag", respectively.

Good night is also an accusitive case, but "nacht" is a feminine word-- therefor, nothing changes. It is Die nacht, and therefor, gute nacht.

And it's spoken as guten nacht in the same way that brittish people say "an hypothesis" Mechanically it's not correct. It's only correct when you speak it.