Such a sick mod, best i've ever seen on this and other forums. A possible idea would be the modularity and DIY element of anything in fallout how it is hastily done and not the usual way. Examples could be a pci-e riser for the graphics card to be in a non standard position, or externally mounted ssds for example. Or simply some metal patches riveted/bolted onto the case.
Would be good if you could do something never done before though to keep it unique and fallout-esque, multicoloured hardware screws could be used aswell, or bigger/smaller ones to make it seem thrown together.
To keep in with the retro-futuristic a dvd burner disguised as a floppy drive or a new component combined with an old one to make it fit.