Let's talk about the transition first. The stock specialized S-Works crank pairs with Specializes OSBB or Over Sized Bottom Bracket. Your s-works crank has a 30mm spindle (BB30) and probably pairs up perfectly with what you have for a bottom bracket - which is BB30 as well. Here is a site with a chart you can use. Use the left column to pick your desired crankset and spindle (GXP or BB30, etc) and right column to find the adapter you need so they pair up with the OSBB if needed. Easiest thing to do would be to find the same crankset in 165mm and install it with the current bottom bracket. Use that strategy for both bikes. If you are switching spindle sizes/lengths then you will also need to change the bottom bracket to match the crank. https://wheelsmfg.com/carbon-osbb-tech
Second, let's look at the 2012 S Works Roubaix. You say Dura-Ace crank so that means it's a 24mm spindle. That means your current bottom bracket has a 24mm hole aka SRAM GXP or Shimano Hallowtech 2. They mean the same thing- GXP/Hollowtech are both 24mm spindle bottom brackets. Which means you should hunt down another shimano crankset in 165mm or hunt down a SRAM 165mm crankset that has GXP in the title so it can be used with your CURRENT bottom bracket. If you find the crankset you want, and it has BB30 in the title, then that means you will need to get a new bottom bracket that is BB30--BIGGER than BB24 (GXP/Hallowtech 2) in order for it to work.