You are correct that OmniPlan does not search the custom data field.
I've attached a simple Applescript that attempts to address this omission. When run, it prompts for a search string, then searches every row in the document for custom data containing that search string in a designated field of the custom data. If none are found, an error message will be given, otherwise all rows matching will be selected in the document. In the script, I called that field "magic token" but of course you should edit it to match your document. I didn't figure out the appropriate incantation to have that be a variable so the script could prompt for it, but maybe one of our resident Applescript gurus can address that. It sounds like that's unneeded in your scenario.
If you don't know how to install and use Applescripts in Omni applications, see the following thread: http://forums.omnigroup.com/showthread.php?t=7453