Rail Pass or individual tickets

Our itinerary end of March beginning of April

Haneda to Kyoto
Kyoto to Mijyama
Mijyama to Kyoto
Kyoto to Kanzawa
Kanzawa to Takayama
Takayama to Hakone
Hakone to Tokyo
Tokyo to Haneda

Should we get rail pass or individual tickets...will we not be able to get seats because we can not book in advance since our pass can only be activated once we are there? What is better economically?

simply use http://www.hyperdia.com and do the math for yourself? just add every ride and then look which comes cheaper. please note that railpass includes free reservation, so if you want to compare you should count the prices including reservations

It depends on your travel duration. If you are traveling all destinations within 7 days, then JR Pass is more economical.

This site has a "JR Pass Calculator" (under Travel Planning\Transportation tab) you can use to estimate the cost of transportation and determine worthiness of JR Pass.
Try it:
http://www.japan-guide.com/railpass/

having a hard time figuring out haneda to kyoto as there are so many different options not sure which does or doesnt go under the pass

Get pass (simple, even within 14 days).

Routes and what is covered - given how much effort has been put into how to use, and the number of questions that always get asked - it is actually pretty simple.