When I was in the market for a new digital source, I exchanged a few e-mails with Dan Wright at Modwright, asking him about the Sony 5400. His response was that the Modwright Transporter to him sounds better than the Modwright Sony 5400. Probably because he is steering customers toward the Transporter, I couldn't find too much written commentary on the web about the Modwright Sony 5400. Instead, I read a lot of glowing praise of the mods by Vacuum State Electronics of the Sony 5400 (both professional reviews and owners' impressions). So if you are considering modding a stock unit, you might want to investigate VSE. That said, Modwright has an impeccable reputation for customer service and a lot of avid fans over on Audiocircle.
I ultimately decided against investing in the Modwright or VSE Sony 5400 mods. Mods certainly have their proponents, but I think they make most sense if you already own the stock unit, pretty much like its sound signature, but want to improve on it and never plan on selling. If you instead pland to have Modwright or VSE perform mods on a new unit, there are more risks involved -- you may not like the sound signature and then may take a big loss when you try to sell it.
FWIW, I ended up buying the PS Audio Perfect Wave DAC & Transport, which can be bought for about a third off the $6K sticker price from some on-line retailers. One dealer who sells a lot of brands, including Marantz and Meridian, told me that I would have to buy the latest Meridian 808 model to obtain a better sounding CD player than the Perfect Wave DAC & Transport.
If you want to spend less, I would probably look at a NuForce-modded Oppo. It is less expensive than the Modwright or VSE Sony 5400, is highly regarded, and sells more easily in the used market.