You wanna Travel through Kerala and Explore it. Just Do it.
Use the Cheapest Means
Public Transport is the cheapest. KSRTC Buses interconnects all the tourism destinations of Kerala. Use local cab services or Tuk tuk for local sightseeing.
Tuk tuk, Jeep, Cab are best for Munnar.
Trekking and Camping is suggestable in Munnar and Thekkady. Jeep Safari programs are a Must Things to Do in Munnar.
Alleppey Houseboat Cruises. I will suggest day cruises at the backwaters of Alleppey or Kumarakom.
If Kovalam beach is in your plan. Go for Poovar Island Cruises.
Kanyakumari near to Kovalam which is in Tamil Nadu can be added to the choice of Destinations.
Spend Enough Time in each destination with a detailed study about it.