I've decided to try "Option #2" with regards to the light engine's optical assembly; namely, pulling the components and designing a single, monolithic print to house everything (PCBs, light engine, microscope objective).

Measured all the inter-element dimensions before I start pulling components, just to make sure I have a record of the "official" setup. I'm going to try removing the PCX lenses from the overall configuration so I don't think I'll need these dimensions, but it can't hurt to have. I also took down the PCB dimensions so I can build a proper housing instead of just using double-sided tape :)

Time to dust off OpenSCAD and start modeling the enclosure!