I have electric water pump in lower radiator hose, since I fitted it heater performance was poor - no forced flow through the heater as with mechanical pump. Since I drilled 2 holes in cylinder head heater performance got worse, sometimes it blows cold air instead of hot. My guess is probably Toyota omitted cyl.6 cooling holes for better heater performance ?? Though with mechanical water pump it shouldn't be the issue.
Here is cooling system diagram
http://www.mk3ukr-supra.com/Cooling System.pdf
Here is cooling system diagram
http://www.mk3ukr-supra.com/Cooling System.pdf