Blender day 1 is a pain in the asterisks ain't it?
I would never pretend to be an expert at blender so, someone better at blender than me may have to take this one but my classic approach is to make sure you recalculate all your inside and outside walls. Then you may just have to delete the offending faces and rebuild them. Make sure there aren't duplicate vertices because that often screws with the manifold faces.
Cleaning up or editing a model that someone else made or has been heavily sculpted can be a really time consuming task. Unless someone who's more knowledgeable at blender has a good trick I think you might just be left with tedious work of deleting and rebuilding.
Also if one or two faces just won't get fixed try exporting and printing it anyway. The program may just be misinterpreting the geometry and the printer won't have a problem.