I've ended up with a simple low tech "just get it done NOW" solution where I placed the two separate 3mm LEDs next to each other. The orange LED (SCSI HDD) is fine, but the green MonSTer CF-card LED is a little faint. No doubt a more modern, higher intensity LED would make up for the less than ideal placement angle.
The HDD LED is connected directly and permanently to the HDD while a home-made connector which takes care of the practical bit of being able to disconnect the MonSTer attached CF-drive LED whenever the MSTE needs to be opened up, allowing the LED to be disconnected before disassembling the MSTE top cover. I used hot glue to fasten the LED wiring to the HDD drive bay.
Not the most elegant solution, but it works (at least until I find a more sophisticated solution if I decide to go that way).
Regarding the PVC grommet: I measured a 3mm opening for the LED (actually the original LED was more like 2.5mm all the way while the 3mm LEDs in my parts box are a little wider at the bottom, but it shouldn't make much of a difference). Around 4mm diameter outside of the mounting hole and around 8.5mm wide at the widest. The metal lug opening's diameter is 4mm.
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Here's the DIY cable I made for the LED which goes to the MonSTer board indicating drive activity from the Compact Flash memory card drive. I used two pairs of SIP sockets for this and heat-shrink tubing.
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Here are the two LEDs placed next to each other underneath the metal lug. Note that I haven't used any hot glue on the LED diffuser plastic so I don't mess it up in case I want to revert my LED modification. Hot glue is used to fasten the wires.
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Finally, here's what it looks like when the internal SCSI HDD is accessed:
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And here's the green LED which indicated CF-card activity from the MonSTer board:
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