35-tone scale in Western Music?

Esteemed collegues, I have prepared a raw introduction to Western tonal structure in my website:

http://www.ozanyarman.com/mainpage/academic.html

Now the issue lies in resolving the obvious discrepancy when modulating from one key to another although the pitches appear to be correct mathematically as well as notation-wise, not to mention theie appeal to the ear. The problem is made clear in simple terms when transposing D,E,F,G,A (6-3-6-5) to E,F#,G,A,B (6-3-5-6)

Cordially,
Ozan