Figured I'd reply to my own message just above for those interested or following my situation. The 'churning' I heard was actually the left fan inside the system, which I managed to disassemble so I could lubricate the sleeve bearing with a touch of mineral oil - now it's as quiet as ever and works great. Also, I ordered a replacement optical SATA adapter cable from iFixit and this resolved my issue of accessing the hard drive moved to the optical slot inside the dual drive enclosure. Long story short - all of my issues are resolved thanks to some disassembly/repair work and new parts from iFixit!
Same issue here unfortunately... new SSD in primary slot is recognized fine and allowed me to install OS X with no issues from USB. However, both during the install when booting from USB and post-install within the full El Capitan OS, I simply do not see any '2nd' hard drive in the system - for the record I just reused the same 500GB HDD that came with my MBP; and I ran the exhaustive System Profiler tests prior to doing any work to ensure I'd have no HW issues/surprises. Sure enough,. I can hear the mechanical drive churning as the power runs to it, so I know it's hooked up okay. For some reason the drive just isn't being recognized by the Mac OS. Hoping someone can help me resolve this so I don't feel bad about spending the [extra] money on the iFixit enclosure system vs. one of the cheaper alternatives I found online, sigh... Any help would be much appreciated, thanks!