going stage 3+ will put you easily over 400 awhp. The a6 has the same engine as the s4, just heavier. There are stage 3 s4's in the 11's, so your mustang could have problems with stage 3's. But its quite pricey to do so

 

plus your audi will put the power down better than the stang

 

You asked about stock - not heavily modded. As stated, going stage 3+ will cost money but give you 400hp. And you'll probably need a new clutch, too. Going with a stage2 GIAC will give you about 70 more hp.

The stock 4.2 A6 should give the 540 a good run, but it's a little slower. Again - weight and having the overhead of quattro.

My A6 is a great sports touring car - very comfortable and quiet at highway speeds. Plenty of performance with the chip. Tops at around 150, but is very quick from 70-110 in 6th gear. It will NOT spin the tires due to the ESP and quattro.

Drive them both and make your decision. You'll pay more for the BMW. So you figure out the value equation.

 

I have a 20014.2 A6 and my older brother has a 2000 540i both auto and he is no quicker than my A6. Everytime we race, it seems to be 50/50 on who wins.