There are several things potentially going on here there are confusing you.
The first that comes to mind is a grammatical point being somewhat obscured by the use of formal structures.
To me, it looks like there are three different types of sentences you're learning to express here.
- Noun Phrase is Adjective
- It is Noun Phrase.
- Noun Phrase is Noun Phrase
These would correspond to the following three rules for Japanese
- Noun は Adjective (い-adj or な-adj) です
- Adjective (い-adj or な-adj) Noun です (Notice this differs from your rule 2)
- Adjective (い-adj or な-adj) Noun は [Noun Phrase] です
These are expressing three rather different ideas.
Examples first in English.
- The red book is expensive.
- It is a tall mountain.
- The young woman is a student.
In Japanese, using plain forms (which you may not have learned yet), these would be expressed as
To move these into a more formal register, you would change them as follows.
- For sentences ending in an い-adjective, the sentence is made formal by adding です
- For sentences ending in だ, change だ to です
So, applying these to the three sentences above (to make them formal), you get
There is no Japanese grammatical structure that is composed as
If you're starting with <Noun phrase>は and ending with です then between the two you need to be saying something about <Noun phrase>.
So, it's ungrammatical to say
The read book is .... <what? you haven't said>
But you can say
It's a red book.
You can also say
The red book is this.
I suspect that the there is a typo in your rule two. It should perhaps read
- Adjective (い-adj or な-adj) Noun です
Notice the omission of the particle は.