How to Encode Consonant Clusters in a Syllable

I tried at least five or six times to make the idea work in a nonhistorical fashion. I basically decided to try and contrive some historical explanation of how the script came to be the way it is. And that meant going back and establishing a proto system. It just, it was so hard to get it where the consonant glyphs and the diacritics felt like they actually belong together in the same script. At this point all I have is a very unwieldy syllabary.