Reddit mentions of Metra 72-5600 Ford Speaker Harness 1998-UP

Personally I'd spend a few more bucks and do this:

• Clarion Mobile Electronics CZ CD/MP3/WMA Receiver : http://amzn.com/B006WVX9R2
  
• Rockford Fosgate Prime Full Range 3-Way Coaxial Speaker - Set of 2: http://amzn.com/B00BF6HVGY
  
  I just figure if you're pulling your stock head unit out you might as well have bluetooth and other modern functions in it.
  
  Heck, you'll probably see a good change in sound just switching the speakers out. If they are the stock speakers in there they are cheap 16 year old cones. To make the speaker install a snap, just use these:
  
  
• Metra 72-5600 Speaker Adapter for Select Ford Vehicles
  http://amzn.com/B001OAB6BW

I just replaced mine in my 06 without the Bose system. The removal and reinstallation is pretty straight forward. I do want to go back with some sound deadening material or a foam baffel to see if there is any better bass response.

I went with these "Rockford R168X2 Prime 6 x 8 Inches Full Range Coaxial Speaker, Set of 2 https://www.amazon.com/dp/B00BF6HVGY/ref=cm_sw_r_cp_apap_bCSfTbRya1zVA "
I also used​ these so I wouldn't have to cut the stock harness
" Metra 72-5600 Ford Speaker Harness 1998-UP https://www.amazon.com/dp/B001OAB6BW/ref=cm_sw_r_cp_apap_HhPhN5qVTdyWy "
You will need to crimp on new connectors for the speakers as the POS and neg are on the wrong sides.

Over all the speakers are on par with stock imo. They are a 50 rms speaker and the stock ones are 25 rms.

I just bought a '14 GT which is essentially the same internals as the 2011. I went with these Polk DB571's. Took me about an hour and a half to install, but it all went flawlessly and they sound incredibly better than the stock crap that came with it. Sync calls now sound clear and nice whereas before they were muffled and flat. They do not need an amplifier and they are so much better than stock.

Also make sure you buy 2 of these as well so you don't have to do any fancy wiring. Each pack comes with 2. And also a set of these so you don't damage anything taking the doors and trunk shelf apart.

Here is a crazy useful video on how to install them.

Total cost for two sets of speakers and tools to install them, about $130. This is of course assuming you have a ratchet set available.

Best of luck! I'm not sure about '06s, but mine required these adapters. Ford used some kind of plug for the factory speakers, and I needed that in order to avoid cutting the door harness.