What is the distance between 2 adjacent waypoints?
The distance between waypoints on a procedure or airway can vary tremendously. For waypoins on a high altitude airway, over 100 NM is common. For low altitude Victor airways, less. For an instrument departure or arrival, 10 to 20 miles is common, especially near the terminal area. On an instrument approach, legs are almost always under 10 miles. So the limit for your application depends on what sort of airspace you're modeling.  At 100NM square, that's more nearly the size of a terminal area than an enroute sector, so 10 to 40 miles is probably a reasonable ballpark.

Might be worthwhile to order an actual IFR enroute chart - they're only a few dollars, and then you have a real example of what airspace actually looks like. Or, any of the free flight planning websites can show you essentially the same thing on-line.