I have done half the trip that you are planning so answering accordingly -
Kochi - Fort Kochi area, eat some amazing fish at fusion bay, see the chinese fishing nets
Kochi to Allepey we went by train.. took us 1 hour Allepey - full day houseboat booked by Spice routes. Ask for one with a upper deck. Allepey to Munnar we went by road. I can provide you with driver details. Munnar - stay at Devonshire hotel. Extremely beautiful view.
We visited a tea factory and took a tour, went to the dam, took a session of Ayurvedic massage, saw a kathakali dance performance