After doing a manual stabilization with position and rotation via the tracking panel, I cannot adjust the stabilisation effect through the effect panel. When I click my footage, no effect settings pop up whatsoever. Am I missing something? Because I'm sure normally I always see the stablisation controls through the effects panel.
No, you are mistaken. The legacy 2D tracker creates keyframes. It's not an effect. Only the 3D camera tracker and warp stabilizer are. Therefore any tweaking will have to be done in the tracker itself before generating the keys or by manipulating the resulting keyframes.