I also got the cases today.
Did I say it was going to be a tight fit?
Basically, I think there is only a single good config. The toroid mounted against the front plate, and the 2 caps and bridges mounted to the bottom panel, right up against the front plate. Thus the PCBs will be moved to the back corner, away from the IEC inlet. It will be close, but it should fit. Remember that diodes emit RF and should be placed away from any input / output lines, and of course the same applies for AC lines.
I really like these cases for the money. They look kinda crappy, until you get them assembled... then they are nice and sturdy. With a nice front panel made from wood, I think they'll be very nice. Also, it's about a small as you can get this project, in terms of case volume... trust me