Matching a McIntosh 275 amp +C50 Pre-Amp +B&W 804D3's w/ spkr cable Transparent?

Ever tried Tellurium Q?  They would be a great match for your gear. 

I also run a MC275 mk V in my main rig and am using AQ Sky between TT(VPI) to Parasound JC3 phono preamp, AQ Cheetah from JC3 to preamp and then MIT Oracle V3.2 from preamp to amp. MIT Shotgun S1.3 speaker cables connect amp to Alon Lotus SE mk ll speakers. I too have a REL sub but it's a Stadium lll and to connect that I use Synergistic Research Tesla REL SPEC Resolution reference. All power cables except two are Synergistic Research. 

I've always found a synergy between AQ IC's and MIT speaker cables and I imagine that synergy would also apply to Transparent as well. One thing I've done with excellent results is upgrade the DBS on the AQ IC's from 72vdc to 100vdc.

It looks like you've put together a nice system and I too would recommend replacing the Nordost speaker cables. I tried those very cables in my system as well and ended up going with MIT due to the attributes mentioned above. At this point may I recommend the following:

> Upgrade the DBS to 100vdc on your AQ IC's if possible
> Upgrade all your component fuses with Synergistic Research SR20 fuses. You could also explore other fuses as well such as HiFi tuning or Iso-clean. SR has the new Black fuse out now along with the Red and they come highly recommended but there is still ample stock of the SR20 fuses which are a major upgrade over stock and they are a lot less expensive than the Red/Black.
> Replace the fuses in your REL T5. I replaced all of the fuses in my Stadium lll with SR20 with excellent results.
> If you're using the stock REL cable, replace it with an SR cable or equivalent. (I assume you're utilizing the high level input for connection?)
> If you are running the stock tubes in your MC275, start by upgrading the KT88's to Genalex Gold Lion KT88's. When time/funds allow, upgrade V1 if you're using the SE(unbalanced) inputs.
> Replace the Nordost speaker cables. If MIT cables are a line you would consider, sign up on their clearance center page and they have some great deals on NOS cables, some discounts as high as 50%. 
http://mitcables-clearance.com/
> Add a motor controller to your VPI Prime if you haven't already. That makes a major improvement to the VPI tables. I use a Walker on my Scout and the difference is not subtle at all. 

You didn't mention your main electrical outlet and if that is still the one that was installed when your dwelling was built and you're utilizing it, that is a major bottleneck for your whole system. Consider upgrading it to an Oyaide, Furutech or Synergistic Research outlet. In fact that would be the first item to upgrade and then go from there.

I know that's a lot of info to digest but these are items that myself and a whole host of others have found that make major musical/performance improvements.

Cheers

**Purist Audio Design dealer disclaimer**

Just installed some Purist Venustas Luminist bi-wire speaker cable for a customer with 804D2s.  "I can't believe how open, detailed, and fulfilling these speakers now sound" was the customers first impression...

Purist has been building the finest cables on earth for over 30 years, I would include them in your cable evaluations.

I run Straightwire Crescendo III balanced interconnects and speaker wire for my Mac system (MC275 Mk VI, C1100, MCD550) to KEF Ref 5 speakers.  This setup is so transparent (for lack of a better adjective) that it reveals everything on an LP or CD, good and bad. 

The best power cord I have encountered is the Clarus Crimson (HC for amp and standard for preamp).  I also use a Kimber Kable PK14 Palladian on my CD player and the background is dead silent.