The main IC is the main culprit usually.
Reflowing is not enough.
Removing the chip, cleaning underneath and soldering back is the way to go.
Looking at the picture, the right side legs doesn’t look to be touching the board.
Wow, this is a beautiful log! I'm waiting to do a Classic -> Classic II board upgrade, so the recap guide is really gonna help. Did you ever figure out what the jumper wires were for – maybe broken traces?