I thought I'd chime in as I'm having a very similar problem as you. The transformer on my TAF blew a bit ago. I finally tracked one down and replaced it only to find that now the CPU won't boot and showed the same light pattern as yours. Up until the transformer went out, the game worked great.

Turns out that the problem doesn't seem to be with the CPU board. I disconnected all cables from the CPU board except J210 (power to the board) and the CPU booted just fine, showing the correct light pattern. I did this because of the following tutorial: http://pinballrehab.com/1-articles/solid-state-repair/board-rework-test/231-testing-wpc-cpu-on-the-bench#blanking

Perhaps you should give that a try to verify whether the problem truly lies on the CPU board?

Full disclosure: I've only been working on this game for the past few months and I'm new to pinball in general in the past year.

I'll update the status of my game as I learn more. I hope that it helps.

No, I haven't quite figured out the problem but I have narrowed it down. After systematically hooking back up all the wires except for the ribbon cable J601 (connected at MPU, flipper and sound - just not the DMD) I get the computer to boot and 5 sound "bongs" which should indicate a ROM failure at U14. If I hook up J601 then the computer doesn't boot.

I'm going to swing by a repair shop in town today and ask for their advice. I'm hoping that perhaps it's just a bad ribbon cable. That might not make sense and just be wishful thinking. But I'm an optimistic person.

I have no reason to think that powering on the game with just the J210 plugged in would fry anything.

You must be incredibly lucky not to have had run across such problems before given your collection and ownership history. Or I just had a spot of misfortune by running into back box detective work after a few months of owning my first game. Either way - I really love the repair side of things and now consider it part of the game.