Learn Russian: Утренний кофе очень горячий.

Утро is a noun meaning morning. Because we are using it to describe the coffee, it changes into the adjective утренний. Many time expressions work this way: if you want to say 'tomorrow's meeting' or 'yesterday's soup', you have to change the time word into an adjective.

Кофе ends in -е, which usually means it is a neuter word. Why do the adjectives describing it have masculine endings?

Кофе is a famous exception in Russian! Even though it looks neuter because of the -е ending, it is actually a masculine noun. That is why we must use the masculine adjectives утренний and горячий.

Where is the word for 'is' in this sentence?

In Russian, we almost always drop the verb 'to be' (is, am, are) in the present tense. You literally just say 'Morning coffee very hot.' The 'is' is understood.

Why do the adjectives утренний and горячий end in -ий instead of the regular masculine ending -ый?

For горячий, it is because of a strict Russian spelling rule: after the letter ч, you can never write ы, so you must use и. For утренний, it belongs to a special group of soft adjectives that always take the -ий ending.