Based on what you say, I would assume you pinched or damaged a flex cable during final assembly. Now that you have it open again, I would double check all the connectors and flex cables. If you can, inspect everything with a magnifying glass or jeweler's loupe. Even tiny scratches or tears to the flex can be problematic.
One thing you don't mention, however, is the battery. Did you disconnect or isolate the battery every time you played around with the flexes, especially the LCD flex. You may have damaged the backlight circuit.
As @benjamen50 suggests, perhaps it is just a firmware problem so worst case, you could try DFU Mode if data retention is not an issue.