I just got an email from NI that I passed the CLD exam!
I've been poking around here for some time, but not really posting much though I'm sure that will change. There's not too many people in the world that know what a CLD is, so I figured I'd come share it here.
I would think that source distribution is your best bet. If you don't like the detailed hierarchy then you may use llb as your destination. You can put each class into separate llbs.
If you want to use the EXE method that I think you would need to run the EXEs and communicate to them with an application reference mechanism and VI server calls. Not sure what you did exactly in the EXE implementation.