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I have had similar issues building workflows. I usually create a "source" column on each of the input streams to help trace problems downstream back to the source files. Another option is to toggle the include filepath checkbox in the input tool. Hope that helps!
I would use the formula tool after the input tool, create a new column named Source, then just use text to give it a name "File 1", etc. If you have a lot of files you're working with it may be easier to just toggle the filepath checkbox in the input tool.