I would suggest you don't go for a toroidal in this design - reason being toroids have higher interwinding capacitance. What this means in practice is more mains-borne noise gets in, and this will suck out the dynamics. Since one of the reasons for going multibit is dynamics, this would be a pity. Besides unless you get a custom wound toroid (always possible but not very cheap) you'd need to use three of them. That's 3X the noise. An R-core is a pretty good choice for this DAC so if I were you I'd stick with it. There are plenty of other ways to enhance it.
Good idea about the larger chassis - saves cursing how tricky it is to get the S/PDIF connector back into position.
I modded the power supplies sure, but when I was really into these DACs I wasn't fully aware of how big a difference PSUs make (hint - huge). So I did stuff like snubbering the bridge rectifiers to reduce RF emissions and I put small value series Rs to provide better attenuation of HF ripple components on the reg inputs. One of the drawbacks of IC regulators is they suck rather badly at rejecting high frequency noise, hence passive filters are needed on their inputs, not just the usual shunt caps. I'd suggest you do the series R (or if you're even more advanced, series inductors) mods on the feeds to the 3 regulators. Also I swapped the regs from fixed voltage (7806 I think) to LM317s which are variable and have the facility for including another capacitor to give much better noise and ripple rejection. They're the same package size but different pin-outs, so its a bit fiddly, I think I turned them around 180o.
Another major mod I did which I've not seen anywhere else is cutting out all the TDA1543s and fitting either TDA1545s (in DIL packages) or TDA1387 (another fiddly mod with small wires as these are only SMT packaged DACs). You can see the results of that on my blog - http://www.diyaudio.com/forums/blogs/abraxalito/871-dacalito-transversal-modification-dac-ah-lite.html