OK, thanks for all that info. First, let me answer your question: "What is a transport?"
Using a CDP as a transport means that you don't use the analog outputs of the CDP, only the digital outputs. When you do this, the sound of your CDP is really the sound of your DAC (which could be stand-alone like Benchmark 1 or Pre, in the integrated amp like the Musical Fidelity A5.5, or in the Pre/Pro/AVR). Doesn't really matter, the key is that the sound is not really coming from the CDP - it's from the DAC.
So, I'd suggest getting the Oppo 980H and use it as a transport to feed your DAC. If you want to get blu-ray then wait for the BD-983. As cheap as the 980H is, you can get it now and get the BD-983 after your system is together and sounding fine. The goal here is to buy one great DAC and not waste money on DACs and analog out for each source component. Hope that is clear.
Indie, you've listed lots of source components with a mix of digital and analog sources. So, as Bob recommended earlier, the Benchmark DAC Pre is probably your best bet here. Because it is a pre-amp, you don't really need an integrated amp like the A5. This is because the A5 is both a pre-amp and an amp so you'd end up with 2 pre-amps. On the other hand, you have a lot of sources and the Benchmark has limited input connections, so the extra inputs on the A5 could save you some cable swapping. Your call, but I'd just buy an amp and connect the DAC Pre straight to it. You can always buy another pre-amp (or pre/pro) later.
So this leaves you with what amp to buy. I recommend you start a new thread and ask what amp to buy to drive your speakers and go from there.
IMO, cables are not that important. By that I mean, do not over spend. Your cables sound fine, and I'd just keep them until you get your system set up. (FYI - your coaxial/optical cable question does not make any sense to me). As Chad recommends, you should map out your system, with connection and connection types (USB, RCA, SPDIF, speaker wire, etc) to get a feel for how your system will operate. If you do it in powerpoint and save it as a jpg, you can post it and get feedback.