I'm not sure about your configuration file, it's possible you need to keep a local copy of that file with the compilation you have. And of course update your install to point to that file.
As far as running lynx, you can update your path to include your home directory before the default - that why when you type "lynx" at the command prompt it will access your local install. However if you're going to be scripting with cron you'll need to call the program by full path anyways - so changing your path won't get you anywhere.
edit your .bash_profile with your favorite command line editor and add a line similar to this
Hope this helps.
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