The duplicate shoes is a known bug that will be fixed in the next update, for now you can just trash them.
"I downloaded single date and extracted it, the files for ultimate and randomizer came included" That is very strange. Just confirming you downloaded "SingleDate_v1.0.1.zip" from https://onesuchkeeper.itch.io/huniepop-2-single-date? I just checked and that only contains the single date dll and images, nothing for ultimate or randomizer.