While I don't own either the Jay's or the Project transports I can state without a doubt different transports do indeed make a difference. I currently have an Oppo 203, an Emotiva ERC-4 and just recently acquired used but in new condition Audiolab 6000CDT transport. Each of these components sound quite a bit different too. The ERC-4 has by far the most digital outputs which includes everything but I2S with the other two coax only. Everything else being equal I much prefer AES to coax and in that vain I recently purchased a 110 ohm AES cable from DH Labs but this one has a traditional RCA connector on the source end with XLR connector on the DAC end. Works perfectly!
Apparently AES connectors do not have the same emphatic impedance connector specs as 75 ohm coax. Regardless I've tried several different AES cables and much prefer the DH Labs, so it was a no brainer when they told me an RCA > XLR cable was available. To those other 6000CDT users in this thread I can only highly recommend this approach assuming your DAC has AES inputs.
No doubt the Jays CDT and Project CDT are awesome if you have the budget and associated DAC with I2S inputs but for now its just too rich for my blood and the Audiolab with modified AES will have to do.
Hope this helps