I also like having the Synthesis and Implications for Climate change combine ideas from the different time periods - it gives paleoclimate studies more of an unified feel, as if it were a real discipline rather than a bunch of people doing their own time-period thing. That's necessary for IPCC, and necessary for the outside community to see as well. So I would vote for keeping the general order, but eliminating the overlap and inconsistencies in ways that seem most reasonable.
2) Concerning the hockey stick (which took up probably 3/4 of the review pages!): what Mike Mann continually fails to understand, and no amount of references will solve, is that there is practically no reliable tropical data for most of the time period, and without knowing the tropical sensitivity, we have no way of knowing how cold (or warm) the globe actually got.