Can you post a picture of the boards all connected up? Have a ball in the trough? Some games require a ball in the trough, just to go in attract mode. Though I keep forgetting if it is only Williams games.

Some Ballys (Centaur comes to mind) require it

If it is required to have the ball in the game, then maybe the MPU is not detecting it. Try reseating your 2 right MPU wired connectors as you try pressing the start button. That would be a sign you would need to repin those 2 wired connectors.

Frontier does not need a ball in the trough to boot.

It sounds like you're only getting 5 flashes, not 6. The first 2 flashes you mention are likely the initial flicker, then the 1st flash, pause, the 4 more flashes.

Can you confirm what you call the 1st flash is of shorter duration than the 2nd flash? If so, then the 1st flash is what is called the flicker, followed by the 1st flash and so on.

Or take a video of the flashes?

Doesn't make sense that something on the machine would be interrupting the sixth flash though, isn't that internal to the board?

The last MPU flash of the power on self test is a check of the zero crossing signal which is derived from the rectifier board. Essentially it's the solenoid 43V power line to the MPU board.

1) Check test point TP5 on the rectifier board for 43VDC
2) If no voltage, check and replace the 5A fuse at F4 on the rectifier board if it's blown.
3) If rectifier board TP5 and the F4 fuse test ok, measure TP2 on the Alltek MPU board for 43VDC (original Bally MPU is 21.5V at test point TP3)
4) If no voltage check for a bad connection between the rectifier board connector J3 Pin 12 to the MPU board connector J4 pin 15 (Grey wire).

Make sure you clear the Altek's memory first via the DIP switches before you set it to the Frontier setting.

Try disconnecting the sound board.

He tried this already.

Yes, definitely do this!

Beyond that, I would also agree with Quench. You are probably missing +43 AT THE MPU CONNECTOR OR BOARD. Just because it is a new board and tests good at the NEW REC. BOARD does not necessarily mean that it's making it's way to the MPU. The connector on the lower left most of the MPU is where +5, +12, +43, and GND enter the board. The pins in THAT CONNECTOR are typically trashed on an early 80's Bally and will need to be replaced.

A lot of the times that lower left MPU connector+pins alone is why early Bally machines fail to boot.

Is there a red LED lit on the Alltek MPU? If so, it indicates a problem.

Then I'd say you are screwed if 3 good MPUs fail to boot with all good voltages.

You ONLY need the lower left connector at the MPU to get a booting state. If you tried that with all 3 MPUs, I'd say you have 3 bad MPUs. Do you have another Bally you can toss the Alltek in to confirm that it's good?

So it's failing at the second last test and not passing the "6th Flash: U12 555 Display interrupt timer"?

Take the MPU board back to bare minimum by removing all peripherals and disconnect J1, J2 and J3 from the MPU board and also J4 from the solenoid driver board and J1 from the sound board to see if it powers up with all LED flashes (flicker plus 7 flashes).

TP2 on the Alltech is for 43v. What does it measure? The 6 flash problem is almost always caused by missing 43v at the MPU.

Try reconnecting those connectors one at a time, see which one causes the issue

Try reconnecting J1 again but disconnect J4 from the lamp driver board.
A peripheral board is shorting pins on one of the MPU board PIAs I/O pins causing that PIA test to fail on power-up.

Ok, the other 2 peripherals connected on MPU J1 are the sound board and the displays. Try disconnecting the sound board first and if still no good then start disconnecting the displays.

Kinda sounds like you need to repin a connector, or two, or more.