It sounds like there is excessive friction somewhere in the system. When you replaced the cable housings did you cut the ends square and file them flat, then install the correct ferrules? Is the cable guide under the BB in good condition with the cable correctly routed? Did you replace the small loop of cable housing which goes into the derailleur and is it correctly sized so that it makes a smooth curve with no kinks? Are you sure that the shifter is paying out cable smoothly? Fiddling with the limit screws will do no good if the derailleur does not move freely across the cogs.