With SH3Cmdr R2.6, Hemisent's sabotage/malfunctions mod will not use the Random folders, thus you will not be not tied to using 52 folders.
But assuming you do have 52 Random folders for whatever reason, you'd add your fanfar files into the existing 52. As you only have 40 files, you can either:
a) leave 12 folders empty of fanfar files in which case if the folder is selected the stock SH3 file will play
b) duplicate some of your fanfar files into the remaining 12 folders.
Using this method you can blend multiple random mods together.
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