Yes, the problem here is that Upload.js is requiring a module from ../utils/file, that one is located in the /node_modules/strapi-plugin-plugin/utils/file and doesn’t exist in your /extensions/upload/ folder.
So here you have 2 solutions: copy the /node_modules/strapi-plugin-upload/utils folder to /extensions/upload/utils or modify the path of the required file in Upload.js and point it to /node_modules/strapi-plugin/upload/utils/file so you could avoid some problems with feature updates.