Why did you disconnect it like that anyway? I just take the two bolts that hold the valve to the intake out... they're easier to deal with... I don't remember how I dealt with the back bolt but I don't remember it being a big deal, biggest problem was the vacuum line to the fuel pressure regulator or EGR valve or something... the one that goes under the upper intake, and I broke the PCV...
I mean, most of your complaints are valid, the long intake runners are apparently good for torque so there's that... when I pulled the upper intake manifold it was just to change the spark plugs and fuel injectors...