Have you done the 100mm extrude test? Heat up the extruder, mark 100mm on the filament from the top of the extruder, manually extrude 100mm. Does it go exactly 100mm? That is really the only setting that can be off. If it does more than 100 you tend to get small holes, less than 100 you can get weak parts. All the other setting had better be exact from the factory, which would give you a perfect cube.
Trust me all printers need fidgeting with. I even got in a fight with my CNC while it was printing this morning. Was just acting weird, printing perfect again, and I didn’t do or change anything.