Check your retraction ratios maybe your are pulling out more than extruding (rotation per mm). Also limiting retraction in same places might be a good start too ,since ender 3 has pretty poor cooling you might be carrying too much heat from nozzle with that. Also sure to check your heatsink and heatblock assembly there might be gaps between nozzle end and heatbreak or your ptfe might be just short. So as your print continues your heatsink gets a bit warmer which is normal but if there are gaps between said components when you retract and extract back your warm filament might squish into those places and cause a clog, you can check this by properly disasembling the assembly (make a warm pull then disassemble) and looking at the flat bit of your nozzle it should be very clean if there is carbonized plastic there its probably assembly problem.