I'm under the assumption that independant travel in Irian Jaya is not a wise decision. Whether it's the environment or humans/animals, one needs a guide. And I "believe" permits are a must have. How to go about these and a vague price per week would be great. And I'd love to hear any previous experiences!
Thanks in Advance!

Independent travel in Papua is definitely possible, though knowlege of Indonesian is a useful asset.
Permits are quite easy to get for most areas.Prices vary enormously depending on where and how you travel.
See the West Papua link in my signo line or profile for more info.

Am in West Papua at the moment. No permit needed before arrival other than standard Indonesian visa. You have to report to a police station as soon as you arrive to get a travel permit for the interior. They ask for a voluntary contribution, I gave 5,000 Rupiah (about US$0.5) but you could get away without giving it as long as you dont come in a big tour group and speak a bit of Indonesian. It's a pretty quick process. Most places you dont need a guide for, even in the Baliem Valley. If you're going more remote than that, ie trekking east into Yali country or further, or trekking in the Asmat / Korowai area. you definitely need a guide. If you speak Indonesian you can just pick up a guy to carry your bag and guide you in a village and pay him 50,000 per day (US$5) or once you get into Yali country 30,000 - 40,000. You also need to buy him food and cigarettes if he smokes. You can stay in local people's huts for 10,000 per night. If you don't speak Indonesian it will all be much more expensive. An English woman who is here traveling alone and staying in the same hotel as me in Wamena is paying 350,000 per day for her trip, which includes food, accommodation, everything. Prices in the Korowai area are even more expensive. The cheapest hotel in Wamena is 100,000 per night. You can sleep in huts in nearby villages for 50,000 per night. In Jayapura / Sentani there are hotels for 50,000 per night. A meal in Wamena can be bought for as cheap as 10,000, but for 20,000 you can get something really nice and a big portion. Trigana flights Sentani - Wamena is 594,000 but the return is cheaper i think. I have also heard of other airlines doing it cheaper (350,000) but havent looked into it yet.