i think you will find that the custom umbilical supplied by ncore that connects the amp w/the p/s will not be long enough to lay out the amp as you have shown in your last drawing. if you want to have the window towards the top, i think you will be better off laying out the modules similar to what i have shown, and turn the amp clockwise 90 degrees, so that the connectors are on the left side and not on the bottom. you may also wanna rotate the amp module itself about 45 to 90 degrees counterclockwise in relation to the p/s, to more optimally use the prowided umbilical cord length.
look at the pics shown on page 11 of this thread, which will give you an idea of the actual length of the umbilical - not sure you would wanna re-do this connector. also, you will find a cut-n-paste layout i did, which could be easily modified to center the amp module by lengthening the speaker and input connection wires; but again, this would leave the connectors on the side of the amp, not on the bottom:

if you want the connectors on the bottom, slide everything down, (making the case larger in this direction), run the power connector up and to the far left of the case, to the side at the top of my drawing, while extending the speaker and input connectors up & to the top side...

basically, what you need to do, is rotate the p/s module 90 degrees clockwise, as shown in your last drawing...
doug s.