I had a transport but never used it much. It's a cool piece of gear and does what it does well. I've started playing with an Android app someone here recommended and it seems pretty cool too...

I've reconfigured twice. Both times it was a major PIA. Both times I was really glad I'd done it.
 
The first time it all began when I simply switched from a USB to a Firewire interface.
 
The FW cable was too short, and when I tried a longer one the interface freaked out. Only solution was to move the rack and computer closer together. I figured if I was going to be shuffling stuff around I might as well move the desk into a better location, for acoustical reasons. But that meant moving the vocal booth next to a window, so I had to cover the window with 703. Now the room was too dark, so I added floor lamps. Not wanting to run the (flourescent) lights on the same circuit with the audio stuff, I built a separate distribution box. I also built speaker stands because the speakers had previously sat on a shelf that had to be torn out for the new configuration. 
 
It all took over a week to accomplish. Only after it was done I realized that the only spot I could put the subwoofer in was the absolute worst place for it. An entirely new configuration would be required. Later, we sold our boat and freed up a garage, so I moved into the garage and applied all the hard-earned lessons - starting with where the sub would go.
 
But you gotta do it, you know you do. Not just for convenience and acoustics, but also for the dust bunnies that gather in places you never look in.
 
My #1 tip: velcro. Color-coded velcro ties are handy, but I'm cheap. In the garden department of your home-improvement store, you can buy this paper tape that sticks to itself like velcro. It's made for tying up tomato plants. It's cheap, can be cut to length and re-used. Great for tidying up cables.
 
For large bundles, there's plastic conduit that's also inexpensive. I ran all my synth cables in them, so when I pack up the synths to take to a gig, all the studio cables remain neatly on the floor, ready to be quickly reconnected later. Colored electrical tape identifies left versus right audio and in versus out MIDI.
 
Also, using conduit makes it easier to keep power and signal cables separated.
 

bitflipper
I've reconfigured twice. Both times it was a major PIA. Both times I was really glad I'd done it.

 
Now this is what I wanted to hear! :) I really appreciate your story. It reminds me of a kid's story. When my kids were young we read them this story called "If you give a mouse a cookie..." and it started with "If you give a mouse a cookie, he'll want a glass of milk." "If you give a mouse a glass of milk, he'll want a straw." and goes on and on. That's been my wife and I's code for when one of these projects snowballs - usually resulting in more purchases! :) I have shloads of Velcro but may use your tip rather than buy more if needed. I also like the conduit idea. I purchased a snake a while back which really made the long run around the room more bearable. It's currently set up so I can grab stuff and leave to play live. My last show was in 2009, so I'm going to abandon that idea this pass and set up for the total convenience of writing and recording. That means a reduction in the racks - moving most everything into the rack system in the desk I have rather than leaving them separate. I'm REALLY stoked. I took off this afternoon, so after I post this I'm heading to pick up some Pho for lunch and them home to start. It will be a lot of work, but I suspect I will feel as you do that it will be all worth it!

bitflipper
It all took over a week to accomplish. Only after it was done I realized that the only spot I could put the subwoofer in was the absolute worst place for it. An entirely new configuration would be required. Later, we sold our boat and freed up a garage, so I moved into the garage and applied all the hard-earned lessons - starting with where the sub would go.

Sorry Dave, I'm confused.. (easily).   You had your studio set up on a boat?

I think perhaps the boat was in the garage so selling the boat freed up the garage. :)
 
Well, it took the entire weekend and some of Monday (all this with the worst cold I've had in years). WOW WOW WOW am I happy. The room seems so much bigger due to the changes, and the fact that some stuff just ain't coming back in. The drum kit sounds just fine, and in fact the kick has more body to it and sounds much better. I have some cabling to do for the guitar rig but it's all in place. It feels a bit like getting a new studio space... A few more hours of work (cabling) and it will be ready to get creative!

Give yourself a little reward for your hard work. Kick back and listen to some of your favorite records. This will begin the necessary process of re-training your ears and brain to what the new configuration sounds like.
 
It may also alert you to any unforseen problems, such as realizing your head is now located in the exact center of the room and every bass note in the first octave sounds like Fish Minor.
 
Yes, Karyn, the boat was in the garage. It was not the studio - not big enough to set up a drum kit in. But at least the kitchen and bathroom would have been conveniently close by.

Karyn
It may turn out sounding way better than it does now..   Don't fight to try to make it sound the same, treat it like you're setting up for a gig and starting from scratch, even if all you're doing is moving some "furniture" around.
 
Good luck!

Wouldn't that be a "good thing", to incorporate into the work? I mean Led Zeppelin can use an entry way to find a far out drum sound, and James can find something else to make the guitar sound closer to your shoe ... FOOT!
 
All the different places I have been and written from, did not exactly "change" what I write. They eventually add more to it, since the space is slightly different, but I have never thought of it as "change" or "different", because the main tools are my hand and the paper, or nowadays, the keyboard and the monitor.
 
Very weird, but yeah, I can see how the different space would sound different when that wave bounced right back at your face, nose first! But, you can use that on a recording, that is hard to create otherwise, I always thought.
 Isn't that called "ambience"?

I have the room set up with a mixing side and a livelier side (more diffusion than absorption) so I was a bit afraid of how that would affect things. It's too early to tell but I think I'm good shape!