Don't change extension_dir. The default value points to the directory which contains all the default PHP extensions, including a bunch of really critical ones like mysql and session. Changing it may prevent these from loading properly, which you don't want.
If apc.so isn't in the location you've specified, either the install failed or you missed a step. By default, a PHP module build will install the module to a "modules" directory in the build directory; you'll need to copy that file to the location you want it.
Finally, the APC configuration values (apc.enabled, etc) don't exist unless the extension is loaded. Right now, the extension is failing to load, so all the configuration values that you're trying to set are just being ignored because PHP has no idea what any of them are.