If I understand this correctly, you should be able to edit the first line of /opt/webwork/webwork2/bin/webwork2. The line
#!/usr/bin/env perl
indicates that the script should be run using the version of perl found in the system path. If you replace that with
#!/path/to/custom/perl
it will run the script using the perl you specify. If you run any of the command line scripts you'll either have to do the same or explicitly load them using your custom perl.
No guarantees that there aren't other places that this is hard-coded, but hopefully this gets you started.