As a last suggestion to Rachel, when you have it set up on the microscope, are you able to see the blue light coming out the objective, and observe the green fluorescence by eye, as it seems you can do with the slide/illumination combination in your photograph?
Have you tried adjusting the position of the LED where it joins the beamsplitter cube, and indeed tweaking the beamsplitter cube? One of the bits of this system that most needs overhauling is the mounting for all the fluorescence optics - if you don’t align them very carefully, you can end up illuminating the wrong bit of the sample, which will massively hurt your sensitivity.
Lastly, are you using the fluorescence parts from the master branch, or the newer version with the lens in? The latter is barely tested and not documented, but we are hoping to fix at least one of those two problems in the next month or so.