Maybe I am not getting it due to my stupidity....but....
Couldn't you just get a couple of horizontal rails and connect them inside a normal rack at the distance needed for a vertical setup of your Mac?
In fact...I think they sell these rails on the Marathon site.
Or another option is to buy a 6u case and turn it on it's side. (thus making it a vertical case....this can easily be done with SKB cases- as they have "pods" on the sides to accomodate vertical positioning)
Another note of interest: I have had my G4 rackmounted (with Marathon rack ears) for about a year now and have had absolutely no problems running it in a horizontal position. If you have one of the Superdrives without the special clips needed to hold media properly...Marathon sells those as well.
Also FWIW: Even though Marathon states the rackmounting of a G4 takes a 6U enclosure......you can actually get away with a 5u enclosure if you don't care to have anything above or below the 'puter.
I had a custom foam padded shock case built....but in reality....a drop or fall would probably still shake a few things up.....computers are just too damn delicate.
EDIT: OK...I just re-read your post....because I am too A-D-D to read completely in one go...
I still think two racks might be the best option. One 5 (or 6)u for the computer to sit vertically.....and a second rack (in the normal position) for the rest of your gear. The other option is just one really big rack, and the horizontal rails from Marathon....then you could rack the monitor and drives and stuff above the CPU.
Or you could call Anvil (or another case builder) and have them make you a custom job....but that will be pricey.
Best of luck