Hi abecker,
The inductors should be in your controller circuit because just as your intuition suggests, you will end up with a short antenna at the input of your box.
If you have room at the reed switch connector, these inductors can be installed at the molex connector you have there by soldering each one inline with the wire going to the switch and the other side crimped to the connector pin. Be sure to shrink tube each one to keep from shorting to its neighbor.
And it looks like you can put your filter caps at each (R1 pullup resistor and PIC input) to the nearest GND.





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