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pretty sure they are the same going way back .... also pretty sure there was a thread on this exact topic not too long ago, try the "Search Community" (top center) and maybe you can find that thread

EDIT: I am talking about just the differential and housing, not the entire axle
 
The differential itself is also different. The 2005-14 Mustang used 31 spline axles/diff whereas the 1979-04 had 28 spline.
The 1994-98 axles are also slightly shorter than the 1999-04 axles. I assume that the axle housings are a different width as well but I'm not sure about that.
Mustang Rear End Gear Ratios & Axle Guide - LMR.com
 
Go to car-part.com where you can search salvage yards across the country. I bought a 60K 3.73:1 from a texas yard for $1000 last year for my wife's 2006 V6 S197 last year and had it shipped. You might get lucky and find one within driving distance.

I just looked and there are several from 2004 Mach 1's with the 3:55 ratio available. Hell there's even one available in Dover, PA with 4:10's!
 
The online locaters can be helpful but if you call or go to a local salvage yard you can get them to order in anything from across the country within their national inventory system and likely have it shipped for free. Pics will often come up on their screen of the actual part. There also seems to be more than one database that yards may use so an individual yard may have access to different inventory. When I ordered body panels for my F150 a few years ago from a local yard 2 doors and a fender were all shipped from other yards with no extra shipping and they were pretty cheap and all color matched. I just had to pick them up at the local yard.
Ebay is also a good source for used parts and entire 1999-04 GT axles can be bought starting at $600 shipped. mustang axle 1999 8.8: Search Result | eBay Some of them will actually be from yards that may or may not enter their parts in a checkable database. A local yard might be able to get you a used axle for even cheaper than $600 as prices vary from one salvage yard to another.
 
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