As mentioned countless times by me in the past, by all means you should make your itinerary first, and then choose the best way to get there.
If for some reason you omitted some important details that would change the equation, then by all means please add them in. But taking you at your word and believing what you've given is accurate, it will cost less money to buy the regular tickets for the Tokyo-Kansai round trip and use the Kansai-Hiroshima Pass for the rest, than the cost of a 14-day JR Pass. Do the math and see for yourself - the numbers are indisputable.
https://www.japan-guide.com/e/e2361_kansai_hiroshima.htmlIf it's more economical and you have the chance to take the Nozomi train (and JR Pass holders can't), it would be in your interest to do so. There are up to about 8 departures from Tokyo per hour (and only 1-2X/hr for Hikari trains), making it much more convenient and flexible for you. (And no matter what, for longer legs, please don't take a Kodama train). If you haven't read the page yet, by all means see
https://www.japan-guide.com/e/e2018_tokaido.htmlfor more info. Not to mention that you won't have to compete against other foreign tourists using JR Passes. And with fewer stops, with the Nozomi trains you will arrive about 30 minutes sooner. The JR West Kansai-Hiroshima Pass also lets you take the Nozomi trains, with the same benefits. Its one drawback is not being able to use the bullet trains between Kyoto and Osaka, but you can still use the limited express trains, which take just a bit longer, or the rapid trains which are no slouch for speed either.
Regarding getting from Haneda into Tokyo, it is simple enough to buy a regular ticket and take the monorail to Hamamatsucho, and then on to wherever else you are going. Or, there are the Keikyu (non-JR) trains from Haneda which may come out cheaper. Or maybe you don't want to bother carrying your luggage (a very wise choice during weekday rush hours), and you can take the orange limousine bus (pricey but convenient) if it goes to, or near your hotel. There are variables like your arrival time, if you want to go straight to your hotel, etc. If you are going to be going all over Tokyo for a few days, then it may be very convenient to get a prepaid IC card like Pasmo or Suica at Haneda - you never have to calculate fares using them. Or, there is a 48 or 72-hour subway pass for just 1200 or 1500 yen respectively and pretty easy to break even on. It can depend where you are going - there often is more than one way to get there. At any rate, your trip is still at least a year away, and you could change or add things on to your plans, so do your research and choose what suits you best.