Why am I seeing extremely high L/D ratio of (e.g. L/D = 90) in my 2D airfoil analysis?
The difference is that one figure looks at 2D flow around an isolated airfoil, where L/D ratios of up to 200 can be reached, while the other figure is for the 3D flow around a whole airplane, warts and all. The additional sources of drag which are absent in 2D flow around airfoils are:

Induced drag. This will double the total drag right at the polar point of best L/D.
Fuselage and tail drag. Of course isolated airfoils only have their own surface where friction drag occurs, but all the non-lifting parts on whole airplanes will bring D up without helping L.
Lift loss at the tips. L/D for airfoils uses the pressure distribution and maybe a drag rake at the windtunnel center section, so no tip effects will tarnish the result, but the outer wings of airplanes will have reduced lift relative to the local surface and drag because of tip effects and to improve stall behavior.
Trim drag: The tail can very well add a downforce to balance the lengthwise lift distribution with the location of the center of gravity. Now extra lift has to be produced by the wing, and both, downforce at the tail and extra lift on the wing, will produce more drag.