Disclaimer. Don't rely on these old notes in lieu of reading the literature, but they can jog your memory. As a grad student long ago, my peers and I collaborated to write and exchange summaries of political science research. I posted them to a wiki-style website. "Wikisum" is now dead but archived here. I cannot vouch for these notes' accuracy, nor can I say who wrote them.
Schickler and Rich. 1997. Party government in the House reconsidered: A response to Cox and McCubbins. AJPS.
The main argument of Legislative Leviathan (C&M 1993) was that the majority party could keep anything that harmed the majority of the majority party off the agenda. S&R's point is that they have cited many cases in which measures opposed by the majority of the majority party have passed.
In their response (1997), C&M allow for lack of majority party homogeneity. S&R believe that this is a significant retreat from their original position. S&R also argue that the evidence they provided in their earlier article was interpreted correctly, contrary to C&M's assertions.
New majorities had different degrees of homogeneity from the parties they replaced. They should have required changes in the rules.
That the majority parties have controlled committee chairs and staff has not meant that they also controlled policy outputs. In fact, in many cases the conservative coalition produced output opposed by the majority of Democrats.
Committee jurisdictions were originally set by a bipartisan committee and actually penned by a member of the minority. C&M would require committee jurisdictions to be consistent with majority party interests.
On defections, C&M believe there are very few. S&R believe that there are many. They are looking at the same numbers. It's all in the interpretation.
Research by the same authors
Research on similar subjects