I used to guide the Alagnek and would recommend that river as a good river. I never floated it because I worked out of a lodge but we frequently had people that floated the river join us for dinner.
The source of the Alagnek comes from two lakes; the Kukaklek (koo-kok-lek) and the Nonvianuk (non-vee-on-uck). At the confluence of the Kukalek and the Nonianuk rivers, the Alagnek is born. The float in from the Kukalek would be about 7 days and the float in from the Nonvinuk would be about 5 days.
I don't know about the float down the Kukalkek because I never took that branch of the river but I have been up (and down) the Nonvianuk all the way to the lake from our lodge and that stretch is easily navigable, with a couple places that will make your trip interesting :).
There are three lodges that operate within the last 4 miles of the river before the bay, the first yo would come to is the Katmai Lodge (where I worked from), the Branch River Lodge (Alagnek means branches), and the Alagnek Lodge. I believe there are lodges on the Nonvianuk and the Kukalek Lakes at the mouth of those rivers you could orient yourself from (they go in and out of business on a routine basis).
You'll have a lot of bears to contend with so pack and live accordingly. On one 4 mile stretch of the Alagnek in the morning hours during the Silver season I walked upon 19 brown bears ranging is size for 900-1200lbs. This is by no means unusual for this area of Alaska so research before your go.
For protection most guides used a short barrel 12 ga shot gun with a pistol grip. Loading the shells 00, 00, Slug, 00, 00, Slug, Slug, Slug. Generally speaking, most side arms won't have much of an effect on a bear if you have to use it. Wear bells, it may sound stupid but get a bell and wear it. Walking through bear grass that's 7 feet tall and turning the corner to come face to face with a bear that didn't know you were there is NOT the right way to make friends with a bear.
I would recommend packing two pair of waders; rip factor and dry out between days plus a repair kit. First aid equipment (you don't get a second chance here). Two types of super glue, slow set with a catalyst kicker and fast set (you can close wounds with the stuff - I glued my thumbnail back on when a king hooked it with it's snagletooth as it rolled). It rains a lot (our weather is born in this area) so make sure you have the necessary equipment to keep you warm and dry. Some of the stuff like a pack tent and the raft you can rent at Kink Salmon, which is where you will depart to most of the float trips in this area (Anchorage to Kink Salmon to your choice).
Branch River Air Service is a highly regarded bush plane service in this area with good pilots. They have more information here
http://www.branchriverair.com/