It seems from your profile that you assume all the sedimentary layers in the Grand Canyon sequence were laid down in one flood event, correct?
I am not sure. I believe a computer model that could recreate a flood sequence that put water 20,000 feet above sea level might help to iron out some of the possible sequences.
I imagine a worldwide flood event that was higher than the tallest mountains would cause crustal deformations and magma incursions, as well as heavy volcanic activity, because of the immense water pressure.
So to answer your question, I think a team of geophysicists and geologists with the finest University, tools and measurement equipment (the reason this hasn't happened yet), we may have some potential answers.
The Grand Canyon is excuse enough for a serious study to be executed, and I believe as more scientists come out of the ID closet, we may see something organized on the scale that would do it scientific justice.
In fact, presuming 20,000 feet of floodwater for which we have no direct evidence doesn't help a bit in explaining the fossilized animal burrows, spider tracks, raindrop imprints, etc. You present no scenario by which it would. Rather, you declare that if we modeled a 20,000-foot high flood with the best brains and supercomputers available the flood scenario would suddenly work. This is a bit like saying that a cold-air balloon would work better than a hot-air balloon if we modeled it with a Cray, if only cold-air balloon technology weren't being conspiratorially denied its fair place.
The Grand Canyon sequence is one of the most closely studied in the world, the reason being is that it's an obvious thing to study! It's sort of 'in your face' in terms of geology, isn't it? ;-)
The problem with interpreting the GC sequence as beeing laid down in a single, catastrophic flood event lasting 40 days is that there is ample evidence of subaerial (ie above water) facies and processes within the sequence. Ichneumon has already posted a great assessment of the Cocconino sandstone, so I won't revisit it, but another example that springs to mind is the Redwall Limestone, the top of which displays classic Karstic topography and also paleosols in places. Karstic features are formed when acidic rain dissolves limestone, so the rock must have been exposed to the elements for a considerable period.
Now, if the Flood Theory for the GC sequence is to hold water (ho ho), then it must be able to demonstrate how the Redwall Limestone was deposited, consolidated, uplifted above water level and eroded, all during a 40-day innundation.