I have the opportunity to buy one of these bikes. Both fit well.
Which would you recommend and why?

Specialized Transition S-works - 2011
FORK
Specialized FACT N'Aero carbon, monocoque construction, 1" steerer
HEADSET
S-Works 1" integrated threadless, sealed cartridge ceramic bearings w/ stainless steel races, conical cover w/ two 10mm and two 5mm carbon spacers
STEM
S-Works Pro-Set, 3D forged, carbon/alloy face plate w/ Ti bolts, carbon top cap, 4-position adjustable
HANDLEBARS
Zipp Vuka Carbon
TAPE
Body Geometry cork ribbon
FRONT BRAKE
S-Works integrated brake system
REAR BRAKE
S-Works integrated brake system
BRAKE LEVERS
Zipp Carbon
FRONT DERAILLEUR
SRAM Rorce, braze-on clamp
REAR DERAILLEUR
SRAM Red

SHIFT LEVERS
SRAM TT, 10-speed bar end shifters
CASSETTE
Dura Ace 11-23
CRANKSET
S-Works FACT carbon, integrated oversize design
CHAINRINGS
53 x 39t
BOTTOM BRACKET
S-Works oversize integrated
PEDALS
Dura Ace
RIMS
Zipp 404 carbon clincher
FRONT HUB
Zipp 404
REAR HUB
Powertap SL+
SPOKES
Stainless
FRONT TIRE
Continental 4000 Grand Prix
REAR TIRE
Continental 4000 Grand Prix
INNER TUBES
Various
SADDLE
Cobb
SEATPOST
S-Works Transition carbon, setback post

OR

2011 Kestrel 4000 LTD - Di2, Zipp Wheels, 3T Bars, TRIMAX
Frame and fork: Kestrel full carbon aero
Wheels: ZIPP 808 carbon aero front/ ZIPP 1080 carbon aero rear (700c clincher), ZIPP Weaponry Hubs
Tires: Vittoria Open Corsa Evo CX 320 Tpi Kevlar 140Psi
Crankset: Vision Trimax carbon 54-42t
Brakes: TRP
Base bar: 3T Mistral pro carbon
Aero bar: 3T Ultimate performance
Stem: FSA OS-99 Carbon w/ Ti bolts
Saddle: Oval full carbon rail / shell (never been sat on!)
Shifters: Shimano Dura Ace Di2-Bar End/TT
Derailleurs: Shimano Dura Ace Di2
Chian: Wipperman Connex (gold) 10 speed
Cassette: 11-23t (gold)

Which one fits your stack and reach requirements better? That one. make sure you can ride either with very few/no spacers (which are very un-aero). Will you/do you know how to use a powermeter effectively?

I agree with Jsiegs... fit is so key with TT bikes. My heart was set on a Felt B2 but I just couldn't get it to fit correctly so I went with the Cervelo P2. Now if both bikes fit you great than I would say the Kestrel specs look superior to that of the Specialized... just my two cents. Good luck with the decision

I like the spec on the Kestrel better, but tend to think the Specialized is probably a more aero frame(I'm not certain and how much it matters to you may vary). Really tough call for me.

I think the Spec is actually a 2010, as they didn't offer the highest end Tranny for 2011.

I think in the end I'd go for the Kestrel, the wheels are nice, Di2 is a plus, it's a pretty cool bike.