It sounds like you're more interested in a strength and conditioning program that won't add (much) size and will still let you run. Anyone who knows me around here knows I have a couple go-to programs, and I'm going to throw them out there:
1. Core Performance - With as much running as you seem to do, this will go a long way to keeping the joints and ligaments healthy while stabilizing and preventing injury. This does include squats and deadlifts, but not at hypertrophy protocols, or you can sub out those lifts for something comparable.
2. Anything by Ross Enamait - His stuff is gear more toward combative and fight conditioning (not fight training), and his presentation is very adaptable (add more strength work, substitute one conditioning day for a run, etc), and the interval work will only help your distance running. The other thing is that his stuff is geared heavily toward working out at home, so minimal equipment, meaning no prescribed squats, deads, etc.
Just my two cents' worth.
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