For the icon and name changes, paste the contents of the "Sydney to Neko" folder (Aka the assets and mods folders) into the same folder with the "payday2_win32_release.exe" file.
For the ACH Hitmarkers, paste the contents of the "Neko#ΦωΦ hit markers" folder (Aka the saves folder) into the mods folder.
Anything besides that goes into the mod_overrides folder.