At the framework level
The basic framework you envision seems to have a certain fixed level of charitable resources (potential "sacrifice"), to be stewarded and spent in a utility-optimizing way over time. Once spent, these resources are gone. In this framework, asking "is the amount I would have to donate to the best charity to accomplish the same benefits as donating a kidney less than the price for which I would sell my kidney?" is a coherent and useful question, because you plan to offset your charitable contributions by that amount ...
Not sure what to say about this. I don't talk about it much with strangers. My friends and family seemed to think that donating a kidney was a bigger deal than giving away or foregoing a lot of income; I don't really agree. Broadly, I think that donating a kidney has convinced people I have more "skin in the game" than just working for GiveWell has, and I can think of one or two cases where this has made them more likely to take my advice on charitable donations. I think that if I were more comfortable talking about organ donation, it would be po...
Just to be clear, I think that in jkaufman's argument, the $400 is not the opportunity cost of undergoing surgery, but rather an estimate of the amount of money AMF would require to achieve comparable benefit as donating a kidney.
I agree that if you had to forego income during surgery or incur other costs, then it would be reasonable to add those onto the other side of the ledger as you propose. As I mentioned above, though, I think that's typically not the case; medical leave policies are often quite generous in these cases, and public funds are available for incurred costs.
A couple disclosures right off the bat: I donated a kidney to a stranger last year and I work for GiveWell (but this post represents my views, not GiveWell's).
I think this is a really interesting and informative analysis (you might also be interested in David Barry's post along the same lines). However, I think these both miss a few important points:
Living kidney donation operations involve significant savings for the health system, on the order of $100,000 (coming from averting the need for dialysis, which is extremely costly) (Matas and Schnitzler 2003
I tried to respond to this issue above: http://lesswrong.com/lw/d4v/altruistic_kidney_donation/6w9j