If the fuel injectors are not operating optimally, you could see them "fail" when maximum load is demanded, i.e., WOT. I don't know if the injectors are balanced as a set when issued with the car from the factory, but you can bet that after use, they won't have equal threshholds where an event is triggered. Simplest thing to try first is to run some Techron or BG or similar quality FI cleaner through the gas tank, see if that helps the hesitation issue. Keep an eye on the spark plugs to see if the engine is running lean/rich. Don't want any plug wet with fuel for sure!
Valves could also be carboned, as Crash pointed out earlier. Common problem with GDI engines. There are solutions from various aftermarket providers to clean up the carbon, or you could have the valves blasted with walnut shell media. If you (or a trusted mechanic) have access to a boroscope, you can check to see if this problem exists in your SHO.
The 1-2 second knock could be insufficient oil pressure at engine start. Sometimes it can be resolved by changing oil filter brands. Most have had good luck with the Motorcraft "OEM" filter, some have had to use another brand to stop the noise. In an extreme/more advanced case, as BiGMaC pointed out, you could have a loose timing chain issue.