In a hydrogen ion pump the energy is used to join small molecules together to make larger ones which factor most likely has the greatest effect on the number of molecules mitrochondria can produce

The factor that is most likely to have the greatest effect on the number of molecules mitochondria can produce is the number of H+ ions moving down the channel. 
Hydrogen ions move from the outer to the inner compartment of the mitochondria through the electron transport system. The main purpose of the electron transport chain is to build up a surplus of hydrogen ions or protons in the inner membrane space so that there will be  a concentration gradient compared to the matrix of the mitochondria. The concentration gradient helps in the generation of energy in the form of ATP.