This is a great question. Everyone under the sun LOVES the post workout shake for recovery/growth but it has been the one thing that guarantees I get a nice layer of fat going in right at the waistline! Ido might have some insights on this with regards to my hormonal status and not responding favorably but if I take a similar amount of solid food and just shift my solid food carb allotment to post workout, that seems to work pretty well.
Another element is work capacity and if you are constantly tanked you will need to dial back the volume and or intensity of the work until you establish a comfortable baseline. In other words, what is an output in which you can go 2-3 weeks without feeling like you were hit by a truck? Find that level and then slowly ratchet things up. Keep in mind that highly eccentric movements such as squats, wall-ball and thrusters will cause much more soreness than DB power snatches, box jumps and rowing/running. Keep an eye on the amounts and types of eccentric loading and perhaps shift to movements that are less demanding in this regard.
There is no doubt that the CF front page WOD produces a high level of fitness...if you manage the ramp-up and individualize it appropriately. It's my understanding the Bulgarians success in O-lifting was due in part to pumping huge numbers of people through the program and the people with phenomenal recovery and mental toughness made it to the top. The WOD is similar in the regard IMO in that it endeavors to push the bounds of human performance...but that leaves some significant potential for crispy-critter status if one does not tinker loading and intensity.
I've tried following the WOD intermittently and found it to be more than I can handle. SOME would say that's because I'm a puss and a weak performer. I'd be inclined to agree but by modifying things to suit my needs I've managed to post 16 rounds of Mary (5HSPU, 10Pistols, 15 pull ups) in 20 min, a 2:58 fran, 3:21 Diane and a few other goodies I'm reasonably proud of. I could not have done that without modifying things to suit my needs. Others follow the WOD as prescribed and have stellar performance. Bully for them. You need to find what works for you.
"Survival will be neither to the strongest of the species, nor to the most intelligent, but to those most adaptable to change."