I'm not sure if this a healthy signal on 9J pin 13, it seems to change when the blanking is going on(45s into the video). I'm not sure how to diagnose any issues before 9J pin 13(signal VYD11?) it seems to be tied to quite a few chips. Is this a data bus? Sorry I'm a total noob, but willing to listen and learn.
You are correct, VYD11 is part of a bus and is used by a whole lot of stuff. One of its main functions is to deliver the Y value to the Y DAC so it can be converted to an analog signal and move the beam up and down. There's a complementary bus (VDX_) that does the same for the X axis. But VDY_ it also is used for things like setting color information, enabling (and creating) the sparkle effect, binary scaling, and even selecting which page of the big vector ROMs at 6H and 6J/K are being accessed. Bit 11 in particular is part of the range for Y coordinates (fed into DAC @ 11D), it is used by the the AVG chip to direct the execution of the vector generator, and of course by the window circuit. So there will be a lot of varying activity on that line.
Whatever is on VDY11 goes into pin 13 of 9J, gets inverted, and sent out of pin 12. You can estimate if this is happening by observing how your probe behaves while on pin 13, and then comparing it to 12. For example, both LEDs are flashing but one is probably brighter because the pin is spending more time in that logic state. Switching to the other pin should show the opposite.
That goes into pin 13 of 7A, and along with pin 12 gets the logical OR operation applied to produce a signal on pin 11. That is used to refresh the flip-flop at 10K, which is being cleared by low pulses on its pin 13. At the proper time, a low blip will come out of pin 8 to allow the rest of the window circuit to sample the Y output at that moment. So make sure you have activity that resembles this on each of those pins, all the way up to pin 16 of 12D.
The rest of the Window circuit is hard to probe without a scope, so just do a visual inspection that you have the right parts installed and all pins soldered.
Then, in the RGB output section, probe pins 11, 12, and 13 of 8K and pins 1, 2, and 3 of 8J. Make sure you have a 74LS00 installed in 8K and a 74LS02 in 8J.
I also took a quick video of the weirdness on Y2, sometimes it's almost as if the leg I'm probing floats(soldered in solidly) while not shown in the video it does seem to behave inconsistently.
Seems fine. The crystal is not 'strong enough' to trigger the logic probe. Check pin 12 of 3D for a nice study buzz. But if your Y2 were not working you'd get no vectors at all.