After running WadSmoosh, you should have a file named `doom_complete.pk3` alongside the `wadsmoosh.exe` you launched. That's the real output of WadSmoosh, that `pk3` folder you found is just the working directory where WadSmoosh extracted everything to.
Regarding the skies, double-check the contents of `source_wads`. I don't recall the exact fault on my side now (its been months) but the issue was that WadSmoosh wasn't finding all the data it needed because I'd messed up a filename. My exact fault probably isn't the same as your exact fault, anyway, so double-check the names and MD5 sums of all the files (MD5 sums can be found on one of the Doom wiki fan sites). Better yet, check the log! That's what clued me in.