Re: gear lube
the lower has a 1 drain and 1 vent plug
the upper has a 1 drain and the top dipstick plug and sometimes a second vent plug on the side.
sounds like you have the drain removed from the lower and the top vent removed from the upper.
the two compartments aren't connected.
you need to take at least 4 plugs out.
Might as well do the intermediate too while you're at it (2 more plugs), and the tilt clutch (2 more plugs). 8 in total now.