I have a Gamoto PID motor controller board. It's a nice board for it's price and I would recommend it but there isn't much active support. It has a 3x4 pin section for analog inputs (shown in picture). The pins have a .1" pitch but they are too close together to use the crimp style Molex connectors I usually use and I haven't found small enough connectors that will fit.
Is there a 3 pin connector that will work with this - or a 3x4 block? Separate connectors are preferable but I'll use what I can find.
This might work for you. You could just cut off the one end connector and use the 3X .1" inline connector. Too bad the color coding wouldn't match your controller's wire order. Some of these SIP connectors have a tiny slot that you can push in and release the wire/pin and reinsert into any other position on the connector.
Your other choice you be to look at servo extension cables at an R/C supply house. These are 3 pin SIP connectors available any several different lengths.
EDIT: Looking closely at your drawing, are the 3 pin vertical spacing truly at .1" spacing? Looks like the bottom pin spacing in more then the top pin spacing, relative to the center pin.