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After I run the wadsmoosh.exe I can't seem to find the PK3 it's supposed to create. Should it be in the base folder? 

Yes, all the IWADs are in the right place so I don't think that's the issue.

Do you see any errors in your wadsmoosh.log after running?

Look closer. It's in the same folder as wadsmoosh.exe and can hide in plain sight with how much is already in there