Our advices about a boat between Iquitos and Pucallpa are very simple : Find the Captain ! Do not believe the sign announcing the destination and the time of departure, neihter the people around the boat, believe what the Captain tells you about his boat (and still !) Pay once IN the boat and to the Captain himself.
Bring water and extra food. Generally the boat leave at the end of the afternoon 6-7PM, take 4-6 days and cost around $20-25, but ask the Captain !! Choose a place far from the engine and the light spot (insects).
Stuart is right for the Cusco-Pucallpa part. I will add this: if you take a night bus, bring your sleeping bag with you.
PS: more info at the Lima Club
South American Explorers,
956 Enrique Palacios,
Tel: 01 447 7731http://www.saexplorers.org
Open: Mon-Fri: 0930 – 1700 (Weds: 2000); Sat: 0930 - 1300