For bent-over rows it is probably best to use them as asubstitute for the power cleans in the original template,which would mean you alternate between them every workout ''A''.With the squats maybe you should slow down the rate at which you are increasing them.Mark Rippetoe told me via email that it is rare for anyone to increase their squats by 5kg a workout for more then a month,after which your gains will begin to slow down.When gains begin to stagnate on this program you will then be able to transition over to the single factor 5x5.
Good luck,ask if you have any queries.