After Re-reading these books a million times and reading tons of theories, I have one that I haven't seen mentioned yet. In CoLS Clary and Johnathan/Sebastian are arguing, and she tells him, "I bet you don't even know my middle name." He answers her with "Adele." He then goes on to say that he doesn't know WHY she was called that because their father wanted her to be named Seraphina. Now, in the ID books, Aloysius Starkweather is shocked at seing Tessa, and is very concerned for her saftey. His granddaughter, who supposedly went mad and died after receiving her first marks, was named Adele. Will and Tessa discuss her portrait when they visit the Institute in York.
Just something I noticed :)