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
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.