I'm still leaning towards a solder problem. The common problems we find that prevent solid joints are insufficient heat and insufficient lead in the solder. You want 900F/500C or so of iron temp, and 60/40 leaded solder is also extremely helpful. Missing one of those elements will make soldering a lot more difficult than it should be. Along with the sufficient heat, you also want enough time for the solder to flow through the PC board holes to really grab onto the component leads. Looking at your board, you can see how this has happened with the LEDs (they have low thermal mass) but not the 431 regulators (slightly higher thermal mass).
More info can be found here:
I've been building this stuff for 25 years and I still have problematic joints here and there.