A couple of notes - the cover is designed to fit flush with the chassis and as has been indicated, all the large caps have to be located on the bottom of the PCB. Additionally, on my unit C11 and C12 were probably .15" or so above the top of the chassis as well.
In lieu of moving them to the bottom of the board, I simply sourced some 3/4" #4-40 bolts from my local hardware store and some .197" #4-40 hex nut spacers from Amazon (100 of them!). The original 1/2" 4-40 bolts holding the PCB had two nuts acting as spacers between the bottom of the chassis top and the PCB. I removed those and replaced them with the new .197" spacers and also placed spacers on top between the chassis and the plexi cover. This gave me exactly the clearance I needed and looks attractive. I reused the locking nuts on the bottom of the PCB.
IF ANYONE WANTS TO DO THIS - I HAVE 92 .197" #4-40 SPACERS REMAINING AND I'D BE HAPPY TO JUST MAIL YOU 8 OF THEM FREE OF CHARGE, JUST PM ME.
(also, if anyone is interested in a McShane matched quad of Gold Lion KT-88's, I posted some for sale in the sticky for it...)