Does the Transport make a significant difference

If you have that DAC you owe it to yourself to get their PWT and connect them via the I2S ports. I guarantee this will be the best CD you have heard. I have a PWT and a Wyred 4 Sound DAC 2 SE with that same connector it sounds very good.

What are the thoughts on removing the preamp and connecting the DAC straight to the amp?

This is variable, some systems sound better with pre while others do better without. Only one way to find out.

I'm currently running DAC direct into amp.

Agree with Rja, active preamp vs direct DAC just try both methods in your system and compare. That topic has been discussed it seems a thousand times on audiogon. The answers never change.

wow some great replies above. my opinion...for what it's worth...is I'd step up the entire digital front end...maybe a used dCS Puccinni...has a pretty good volume control built in. Then down the road a preamp.

I do like a preamp vs digital volume control...but again...in a priority I'd do something like a used dCS Puccini first...get the source as best as you can first.