Depend on what rules you use. Around here we use AKRA rules, so the only real difference between a box stock and clone is the pipe, jetting, air filter, flywheel and clutch. Clones use big pipe, bigger jets, aluminum flywheel, air filter and adapter, and a disc clutch. Box stock uses weinie pipe, stock airbox, steel flywheel and stock timing, shoe/drum clutch, and stock jetting.
Clone is a general classification of engine that is a copy of the Honda OHV engines. Box Stock is the set of rules that they run under. Some people use clone as the name of a class that is closer to stock out of the box.
If your track has two classes, clone and box stock...there might be a slight difference that you will need to talk with them about.
At Dawgwood, box stock runs EL tires and Clone runs HT3s....everything else is the same this year