This work (which is still in progress, of course), was written up in the
article "The Wisconsin integrated cropping systems trial: Combining
agroecology with production agronomy", by J.L. Posner, M.D. Casler, and J.O.
Baldock; American Journal of Alternative Agriculture 10(3):98-107 (1995).
Another study, begun in Virginia in 1988, was already mentioned by a previous
respondent. Besides the report mentioned, a possibly more accessible write-up
is "Whole farm systems research: An integrated crop and livestock systems
comparison study," by J. Luna, V. Allen, J. Fontenot, and others; American
Journal of Alternative Agriculture 9(1-2):57-63 (1994).
Finally, reluctant as I am to admit it, worthwhile research in this area is
(occasionally) published elsewhere than AJAA. The mother of all long-term
studies of "alternative" (specifically organic) systems is the famous
Haughley experiment in England. I don't have a ready reference, but no doubt
you can get information on it from its sponsors: Soil Association, 86 Colston
St., Bristol BS1 5BB, Great Britain; firstname.lastname@example.org.