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.
This was happening to me; I had to perform a search on the entire C:\ drive to find where they were being put.
Try looking in C:\Users\<windows account>\AppData\Local\VirtualStore\Program Files (x86) and you should see the name of whatever folder you created to house the wadsmoosh files
edit: right click the .exe, goto properties, select the compatibility tab, and check "run this program as an administrator". that should allow the program to write to the folder it's in.