I too have a Cannondale tandem with the cable routing as pictured by Scraper. The shifting has worked fine, with an occasional adjustment, for several thousand miles.
Originally Posted by
milktree
...trimmed/squared/polished all the cable housing ends and replaced the endcaps with aluminum ones
Are these the correct ferrules for the cable housing you are using? Most modern housings require a plastic ferrule that is designed to keep the individual strands of shifter housing wire from slipping past the end of the housing plastic. Make sure you have the correct ferrules for the housing you are using.
Other things to check:
Did the previous owner replace the shifter cable housing (linear strands) with brake cable housing (coiled flat wire)?
I concur with the previous suggestion to replace the rear section of cable housing and its ferrules. This area is a frequent culprit and the replacement parts are cheap. A housing that is too short can cause binding and a housing that is too long can flex laterally causing incrementally less pull at the rear derailleur.
Brent