I would suggest starting from the town of Balingup (240km south of Perth) and ending in Northcliffe further south. These are remote parts of the track but also take you through Pemberton, you can stock up on all supplies there and it is a beautiful little town. You will hike through a lot of old growth forest and be rewarded with the beauties of of the Kari forests further south.
I recently got back from a similar hike although we did that distance in about 8 days give or take, I have through hiked the Bibb (2011) and must say for a 2 week experience this would be my pick. Walpole to Albany would be another great section to do as you will be on the coast for most of the time and you get to tip a few back in celebration at the end.
You should contact the BTF, (
http://www.bibbulmuntrack.org.au/ ) they can help you with any trip organisation.