Yes, you are 100% correct in that there are multilateral disputes on the sides of most parties in the region, often many having similar and competing/conflicting claims on the region's resources. Not just natutal gas and oil R & D, but other items, like fishing rights, the nature and scope of each nation's EEZ, and other regional energy and power issues.
I think the trick is to carefully assess the major points of contention (and sources of potential conflict) and the creation of security measures that realistically deal with each potential problem. You are correct, the rub or "fly in the ointment" is Japan's legacy from WW-II (and before, also). Would-be partners in an effective security arrangement are reluctant to get too close to Japan, or aid and abet in the creation of a new, malevolent Japanese Empire.
The truth is that Japan is a hard-working and industrious country that has clearly proven itself as a trusted and trustworthy business partner and security co-guarantor in the region.
The trick is to get every ally to see it that way. In light of the massive Chinese military buildup of the last few years, this issue is becoming more pressing as each day passes.
I do not know exactly when or where, but I think the trend in this situation will produce election-defining events leading up to the 2008 elections. I think the Chinese hope that not to be the case, preferring to not have such events affect our next presidential selection. But I think other's reactions to China will cause China to try to play its hand a little too strongly, a little too soon, rather than later. Already they are trying to line up Russia to form joint naval "security" operations from the China sea to the Taiwan straits.