Does anyone know how to exclude customers that have gone through a workflow in a customer search? i have tried filtering the criteria to workflow fields... workflow doesn't equal said workflow. however customers that have been in that workflow still appear in the search

You can have checkbox and tick is when workflow run on that customer and then exclude the one with the checkbox from the workflow.

you should also be able to use the workflow history join which contains filters for workflow name, date entered, date exited to create a combination of filters that work.