Hi Soulman - welcome to the wonderful world of pinball machines throwing a wobbly

Don't panic , it happens and you will get it sorted out.
As others have said the original power supply boards can be problematic , however you have a replacement which *should* in theory be ok.
I have had a Star Wars machine exhibit what could only be described as a mental breakdown with very odd behaviour across the board ....sounds/lights/mechanisms all going crazy . It turned out to be simply a failing ribbon cable. If yours are old it could be worth just investing in a new set to eliminate any potential issues with those.
Regarding the CPU lights, yours look correct , this info taken from Pinwiki
www.pinwiki.com
5.6.1 Data East CPU Board LED Flash Sequence at Boot Up When Working Properly
View attachment 243742
Data East CPU - Location of diagnostic LEDs
Much like the Williams System 11 CPU, the Data East CPU performs a basic diagnostics procedure and produces a series of LED flashes to indicate potential boot issues. The CPU automatically tests the PIAs, RAM and EPROMs at each boot.
With all tests passed, the LEDs illuminate in the following sequence at power-on:
- The PIA and +5V LEDs illuminate immediately
- Approximately 1/2-second later the PIA led is turned off and the Blanking LED illuminates
- +5V and Blanking LEDs are illuminated until the game is turned off.
- If a failure is detected on major board components, the PIA LED will display a flash code: