If no one's not responding, it means either three things.
1. They don't know how to solve your problem.
2. They're looking into it.
3. A person who knows isn't currently online/reading your post.
Please be patient.
I don't know how to use a custom slot. But the only thing I can think of is the stage expansion code.
What I did was replace my least favorite stages or inaccessible stages (i.e. Luigi's Mansion, which keeps freezing on me) with the stage I wanted to download.
I recommend the stage expansion code that can be found on this page.
How to edit it: http://www.smashboards.com/showpost.php?p=11570864&postcount=100
So you would first get rid of a stage you aren't using and replace it with a custom stage id.
So if you wanted to get rid of Final Destination, you would replace 00 with any one of these:
2A2B 2C2D2E2F
30313233 34353637
38393A3B 3C3D3E3F
40414243 44454647
48494A4B 4C4D4E00
The 1B and 1C preceding this are Snake's and Sonic's.
Then you would rename the stage you want to download to STGCUSTOM## (the number being the number you put over the 00).Edit:
It's working perfectly for me. I put it over Final Destination's slot. Maybe it's a code you have?
Edit:
Even works over Slot 0A.
Did you try temporarily using the original common5 (backup your current one and get a original copy)?
What about using a unmodified custom sss?
If it's common5, it's because of the file size limit.
If it's the custom sss, well, then I don't know.

Finally, did you try renaming it? I renamed it to STGCUSTOM0B since I already had a 0A.