Can anyone help with the issue of permits for those more difficult areas, for example Carstenz Pyramid. Is there a single point of contact that can assist with permitting only for expeditions. Thanks for any help.

I looked into this a year ago, here is what I made of it all:
You would need to go to Jayapura and get lots of permissions, permits, pay lots of "fees" and then (if it somehow worked) charter a heli to the base (or trek in for 5 days). You may even have to go to Jakarta for all of the gov't ministries red tape. There is no office for expeditions, you will have to do it all yourself if you try. There is a war between the Indonesian gov't and Papuans, and the mine 5 km from Puncak Jaya (the largest gold mine in the world) is at the center of the issues. The red tape stems from it being a very corrupt country, and in one of the most difficult areas of it-- not mountain safety. Also, if you don't speak Bahasa Indonesia fluently it will be nearly impossible. For this reason most people just fork over the cash. You may try contacting an Indonesian guide service about trips, which would probably be cheaper than a Western operator.

Thanks Andrew, that pretty much sums up my research, a local company or guide service with a good track record seems to be the best way forward.