How do I connect a separate CD transport

You could if you could find a tech that could add a digital INPUT to your unit. It might cost more than it's worth, but I'm pretty sure it could be done.

Yes if the CD player has an output that is compatible with the input on the DAC/CD player you want to interface with.

I can't recall anyone ever mentioning that they had a digital input added to a CD player that didn't come with one from the factory. I'm not saying it's impossible, but I would think that some people would have spoken about having done it if it were practicable. Now that I think of it, Musical Fidelity put out a bunch of expensive CD players with bad, irreplaceable transports and they had to be thrown away when they failed, as I recall.