You may already know this but Test Point 3 is a different source of 12V. It is the "Digital" 12VDC and is actually regulated by Q2 (7812) which gets its source voltage from the +18V for the lamp columns.
Of course, since your J118 12V (which is unregulated) is measuring less than 12.0 V, you are not back-feeding the regulator with any power. Instead, the regulator is feeding everything on the playfield that uses the unregulated 12VDC on J116, J117 and J118.
I didn't notice if you checked or already changed BR5 and/or C30 and F116? If you now have 12.6VAC with the Thermistor jumpered, you should have well in excess of 12V (probably closer to 15) at TP1 if the bridge, cap, fuse, and connections at J112 are good. Unless you have a bad fuse (not actually blown), bad fuse clips, or bad connection to J112, I would suspect your bridge has one bad diode in it, or C30 has dropped well below its 15,000ufd rating.
The 7812 is only rated for around 1 amp. Since by feeding this regulated voltage to the playfield, you are now powering the LM339's as well as all of the LED Emitters. The low voltage to the emitters (which are not regulated and their output is directly related to the +12 V Power they get) is why your optos are barely at the edge of their working output.