Well I finished my mod. You have to remove the RCA connectors on the iqAudio board and chop off the header pins as these stick up too far to fit in the case. You also have to remove the line out and composite video connectors on the RPi itself. (So you're modifying both PCBs to use this case, you'd better be fairly sure you want to do it!)
Firstly you need to get a file and enlarge the semicircular cutout for the line out connector as this is smaller than the composite RCA connector and a panel-mount RCA connector doesn't fit.
I then got a twin-core shielded cable and connected it up, splitting the earth at one end of the cable into 2 braids to attach one to each RCA connector ground, and leaving it as one braid at the other end to connect to one of the original RCA connector ground points on the iqAudio PCB. One of the RCA connectors was arranged so it was grounded to the chassis (it helps to get a good ground if you scrape away the anodisation just around the case semicircular cutouts) and the other one had the insulating rings left in place. This arrangement avoids any possibility of ground loops.
Another thing I did, just because I'm paranoid, was to take some copper foil tape of the kind you use for preventing slugs getting into flower pots or shielding guitar electronics cavities and use it to shield the iqAudio outputs from any noise that might be coming off the voltage regulator heatsink. To do this I scraped back a bit of the anodisation and bent a part of the copper tape back on itself (the glue on the sticky side appears to be quite a good insulator so you won't get a good connection through it) and attached it to the lower part of the chassis, and held it in place with insulating sticky tape. The rest of the foil was wrapped in insulating tape to ensure it didn't short anything, and placed so it lay between the regulator and the iqAudio board above it.
It looks like the mod above also changed the power supply as there's an extra connector installed on the end. I haven't done that as I'm quite happy with the beefy micro-USB wall wart PSU I'm using, but I might look into adding a shutdown switch mod at some stage.
It's a really nice look now, you see the glow of the LEDs through the holes in the top which goes nicely with the glow from the tubes in my Tubelab SSE amplifier

So now I have an entirely homemade audio system: the RuneAudio source, the Tubelab amplifier and a pair of Fostex 126En full range drivers in a hybrid bass reflex / horn enclosure.