stou,
It's extremely difficult to determine the relative sizes of the pilot jets by eye (it can be done with the the main jets, though). The problem is that you are looking through 3 holes which all have to be lined up perfectly; the bottom end hole, the orifice, and the top (tube) end hole. Sometimes the pilot jets are partially clogged too, which makes it even more difficult.
The throttle valve piston is correct, and looks in very good shape. According to my notes the 271303 needle is the richer of the two '74 CR125M needles (the other is the 273003). Could your other needle be a D42? If so, it's the replacement needle that came in the Keyster carb kits. You may want to try this needle, it's leaner everywhere and you might like it better.
Just FYI, the carbs with the 28mm pilot jets have the pilot jet off at an angle like yours; the later carbs with the 32mm pilots have it directly in front of the main jet, centered between the floats. I don't think the floats being 2mm off will make a huge difference, but I always set mine exactly to 20mm so I don't wonder about what difference it
might make.
I wouldn't use the BR9ES - the R stands for a built-in resistor, which isn't a good idea with the CR125M ignition (which already has a resistor in the plug cap). It's also not a high performance racing-type plug, which IMO is what you really want to use. If it were my bike I'd use a BP7EVX (non-resistor, projected nose, platinum center electrode) if you can find one, which is what I use in all my Honda motors; it starts easy, never fouls, and has slightly more low end.
A good starting point on the ignition is to set the piston exactly at TDC, then align the stator mark precisely to the 'T' rotor mark. It's got to be exact; if the mark is just .020" off, it changes the timing quite a bit with a small rotor like this.
Ray