UPDATE!
I've finished enough features to release an Alpha. There's still some more stuff I want to add but I'm satisfied with it enough to fully release.
Instructions
Download:
http://www.mediafire.com/download/63a28mdt3brgiss/PM_Custom_Stagelist_Creator_Alpha.zip
BrawlBox v0.76b:
https://github.com/libertyernie/brawltools/releases/download/v0.76b_h2/BrawlBox.v0.76b.Hotfix.2.exe
1) Extract the contents of that zip to a folder. You should see the file "index.html". Open that up.
2) Use the drop down menus to create your stagelist. If you would like to color code the textures, click "Use colored stagelist textures"
3) Click "Generate codes" and if you had the stagelist textures checked it will automatically download a file called "stagelist Textures.bat". SAVE THIS TO THE ROOT OF THE EXTRACTED FOLDER
4) Highlight and copy all the codes that were generated underneath your stagelist.
5) Open RSBE01.txt and scroll all the way to the bottom. You will see a "Custom Stage Select Screen" code already there. Replace that entire code with the code you just copied from the webpage.
6) Save that text file and drag and drop it onto "gctconvert.exe". This will generate a file called "RSBE01.gct".
7 (optional) If you chose to use color coded textures, run the "stagelist Textures.bat" file (sorry this is Windows only for now)
8 (optional) Open sc_selmap.pac and right click on "MiscData[80]". Click "Replace All" and then find the "miscData80" folder inside your Custom Stagelist Creator folder. Click ok and click ok again when it prompts you. Save and close this file.
9) Put RSBE01.gct in the codes folder on your SD card. Put sc_selmap.pac in the folder: SD:/projectm/pf/menu2/ Both of these files are necessary for this to work whether you modified sc_selmap.pac or not.
Some important notes: Putting Training Room on your Stagelist will cause a bug in My Music. This has a band-aid fix in vanilla 3.6 but unfortunately there is nothing I can do to fix it in custom stagelists. Also including the same stage on page 1 and 2 will over-write the texture and make it banned.
Let me know if you guys have any more questions. I've made a tutorial video to show how this new version works.