It is most beneficial to develop trills between adjacent fingers, so between 1&2, 2&3, 3&4, and 4&5, as this promotes incredible independance between all the fingers.
It seems far beyond my ability though to control the loudness/softness of the trills
It sounds to me like you are playing the 3rd movement of the Waldstein sonata? Is this so? Because there's one part (the main recurring theme i guess) that seems to fit your description...
I trill best with 1+3 and 2+4. Most powerful and fast, maybe because of using the wrist in the former and having the direct collision from the directly positioned fingers in the latter.