Kindly let us know where you get the new C1 (C15 ?). I suggest you replace Q3 before you go live with kilovolts through the new flyback transformer, otherwise you could be up for a second new flyback transformer.

You might also look for black marks or stains or charring on the PCB side of the white vinyl sheet attached to the analog board. 

You can find this same information in Larry Pina's book, Macintosh Repair and Upgrade Secrets.