I gather that your pulse generator is a resistor-capacitor timing circuit with the TO-92's handling swiching duties to trigger the jammer (er, excuse me, transponder) and I'm wondering why not use a 555 or 556?
I use them a fair bit to make adjustable PWM type circuits; by using a 556 I can have one section generating a frequency that is adjustable via a pot which feeds into the trigger on the second section which ouputs an adjustable pulse width also adjustable with a pot.
PS, Cool Project!









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