Ok. Now assemble U1, U2 and U6, and try to boot.

Try to boot with just 3, 4 and 5

That's the wrong JED file!
The read back JED is "V4_50ac" (thats an older revision).
Please use "P4_52", which I have sent.

And please check the other GALs as well, make sure its the latest revision.

Both sounds good to me. Please read back the JEDEC from the GAL U4 and send it to me.

Strange. The only explanation I see is that something went wrong with the programming.
Which GAL and which programmer are you using?

The very same U4 as before? Or a new U4?

Let's fix U4 first. Get another GAL (not the U4 you are using right now), program the P4 JEDEC, and try again to boot.

That's weird. Check the voltage at U4 pin13, should be high. Then all outputs of U4 should be tri-stated, essentially the same as if there were no U4 at all.

Ok, add GAL U4 and try to boot

Next: Remove the U5 jumper wire, and assemble U5 instead. Try to boot.