MPU Led flicker on power up then 3 LED flashes means the game has detected an issue with the 6821 PIA chip at U10.
Now you've already changed U10 so the issue is probably not the chip itself.
A test failure of the U10 chip on power-up can occur if there is a short circuit external to the chip.
U10 controls all the game switches, lamps and sections of the displays.
Your next step is to isolate all these components to narrow down where your short circuit is.
So with the power off, disconnect the J2 connector, J3 connector, and J1 connector off the MPU board and power up. This is the playfield switch harness, cabinet switch harness, and lamp/display control harness respectively.
Power the game on and see if you get the MPU LED flicker then 7 LED flashes.
If you do, power off, and reinstall one of those connectors at a time until you find which connector causes the MPU LED to flash only 3 times.
My money is on one of the LEDs you installed on the playfield has shorted to one of the playfield switches.