We installed 3.4.c x64 from a backup of our x86 3.4.c server to see if it was a 32 vs. 64 bit problem. It was not, the missing content was no longer missing. We did notice that for 3.4.c the Web Quick Start was set to install by default. For 4.0.e, the default was *not* to install Web Quick Start. When 4.0.e was installed with Web Quick Start our problem was resolved. Not wanting to have to start the production upgrade over from our 3.4.c data, we tried installing the Web Quick Start as a module on a 4.2.c server we used for testing. Once the module was installed our missing content came back!
I can fairly confidently say that we have not intentionally used Web Quick Start. Why some of our content depended on this module and other content did not will remain a mystery unless someone on this forum takes enough interest to post the answer.