What I like to do in instances like this is apply Maximum Black Generation to the file which will help separate the Custom Green from the Black.
It's fairly easy to do and it will still keep your transparency.
1. Go to Edit > Color Settings, and where it says Working Spaces, click the CMYK pulldown menu and at the top will be a "Custom CMYK" setting. You'll get another dialog box in which you'll select "Maximum" for the Black Generation.
2. Open the file and convert it to Lab or RGB and then convert it back to CMYK.
3. Copy the Yellow channel and then double click on it so you can make it a spot color of your choice.
4. As DCurry said, do a Select All and delete all of the pixels on the Cyan, Magenta and Yellow channels.
Caution! After fixing your file, make sure you go back to your original CMYK Color Settings profile. If not, the next time you convert an RGB file to CMYK, it will desaturate the file and lose most of its color.
Hope this helps,
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