Finally getting back around to this project while I await some missing stuff for 400 board.
My replica 540B has been gathering dust for too long now. For the past few days when I have had time, I've been examining the signals with my oscilloscope to figure out what's wrong with it.
I spotted a solder bridge attaching pin 11 of U4E (the signal known as /COL_CLR) to some other signal that was chronically low. The result was that the output of the NAND gate on pin 11 would never go above 1V, and thus never trigger the master reset on three of the 74LS163s. This cascaded into the END_BLANK signal never triggering, so the signal would be stuck blanking the video forever. The solder bridge is marked in red.

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After that was fixed, I started to see more sane signals in a few places, which is promising! I've also noted that adjusting the color phase trimcap is very difficult, it requires alot of force, and just the right screwdriver, and I usually end up capacitively coupling the screwdriver to the trimcap which throws the timing off. I feel like I'm right on the verge of acceptable color, but I can see something on screen finally. It's yellow! However, I'd like to replace that trimcap if possible with something higher quality, and I'm open to suggestions for reputable parts.
The Sam's C4P manual that I should be seeing horizontal sync pulse of 4.7microseconds from U4B pin 12, per NTSC spec. I'm seeing closer to 8microseconds. I'm also seeing a vertical sync pulse on U4A pin 12 of close to 360microseconds rather than the suggested 300. I know it says "approximately" in the manual but my inner broadcast engineer is mad at me. Would you say these values are common for 540B build?

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In looking at the video signal output by my board on my oscilloscope, I'd say it's getting closer to sane. My monitor accepts it, but I can't see the color burst or anything approaching a front or back porch on the scope. Sadly I'm not yet seeing anything on screen but a solid color.
I've also gotten frustrated trying to read the schematics within the Sam's C4P document floating around, as they're split between pages within the PDF. Solution? A little photoshop and the 540B schematics are now glued together into two contiguous pages, making it easier for me to follow signals. I imagine the original physical copy was one bit foldout. Maybe they'll help someone else.