I don't think this is the case.
IIRC, I could only ever see a pulse from one leg, and only with a scope.
Once you get to Z3-6 you should always be able to see the pulse.
Pin 37 of the 6502 will be pulsing too. Pin 39 provides the phase 2 pulse.

Since some of the parts in the reset section were corroded, and you removed them, I'd scrape that entire section per the PinWiki and replace it with a DS1811.
See: https://www.pinwiki.com/wiki/index.php?title=Gottlieb_System_80#Using_a_Reset_Generator_for_the_CPU_Reset_Section

You'll still need to make sure that Z2/Z3 and the three resistors are doing their jobs in the reset section.
--
Chris Hibler - CARGPB #31
http://www.ChrisHiblerPinball.com/Contact
http://www.PinWiki.com - The Place to go for Pinball Repair Info

There is nothing wrong with the clock circuit. You can rule that out.
The reset circuit is suspect.
You can manually ground pin 40 briefly when the game fails to boot. If the game boots after that (every time) then the reset circuit becomes a strong suspect.

I almost always scrape the parts and use the DS1811 equivalent (noted in PinWiki). At the very least, it reduces quite a few parts down to a single component.
--
Chris Hibler - CARGPB #31
http://www.ChrisHiblerPinball.com/Contact
http://www.PinWiki.com - The Place to go for Pinball Repair Info

I wouldn't worry about the hot zero.
It is being displayed prior to the CPU getting hold of the board circuits.
The modern reset generator takes about 1/2 second to provide the RESET signal, and that is why the hot zero is lingering. No biggie.
--
Chris Hibler - CARGPB #31
http://www.ChrisHiblerPinball.com/Contact
http://www.PinWiki.com - The Place to go for Pinball Repair Info