This is a pretty good guide of all the national parks. It may not have the most detail for each that you want but it has a lot of information. It's sort of a jumping off point.
http://www.amazon.com/Your-Guide-National-Parks-Complete/dp/1621280004
Well, the NPS website is invaluable to me when planning trips to the parks. It tells what trails are open, weather, lodging, animals, climate, etc... https://www.nps.gov/
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If you can get this book, I highly recommend it too. I own it and refer to it when planning trips, in addition to the NPS site. It has a lot of the same info the NPS has, but also has other recommendations too, like restaurants and hotels in the surrounding areas, where to do other activities (kayaking, horseback riding, climbing, etc..) https://www.amazon.com/Your-Guide-National-Parks-Complete/dp/1621280004
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Also, there are bloggers out there who have completed all the parks and written about their experience in each one. In addition to the 2 aforementioned resources, I always refer to this couple's blog: http://switchbackkids.com/ . They spent a significant amount of time in each park 5-7 days or so and have good hiking and camping recommendations for each one, in addition to videos.
I'm really into national parks and trying to visit all of them. I have this book and it has been a great resource for me! You can also find a lot of good information on the websites for each park.
Be aware that the parks can be very spread out from each other and you should generally expect to do a lot of driving. You may want to choose a specific region you want to explore. Here's a map I made with one route I recommend to explore some of the Southwest. I'm dreaming of doing a road trip to hit all the California parks someday.
Get this book if you don't already have it. . It has great maps and itinerary recommendations that will be super useful for you.
In RMNP, I'd recommend hiking from the Bear Lake Trailhead. Lots of beautiful alpine lakes and though it's at 10,000ft elevation it's not too strenuous so you should be ok. Trail Ridge Road is a great scenic drive in the park, and it usually opens at the end of May. Be aware if you are camping around RMNP it will be cold at night in June, probably lows around 40. You'll want a 3-season sleeping bag.
Not sure what your timeline is here, but plan on spending a couple days at Yellowstone. This park is HUGE and just driving around to see all of it takes 1 day. I've heard 90% of park visitors never get more than 0.5 mile from the road, and you don't want to be like that, do you? At least 2 days, I'd recommend 4. You can easily spend 1 whole day in the geyser basins by Old Faithful (lower, midway, biscuit, upper). 1/2 a day at Canyon. 1/2 day at Yellowstone Lake and West Thumb geyser basin. Don't miss the Norris Geyser Basin, I thought this was one of the coolest thermal features. If you want to do a longer hike, Mt Washburn is about 6.5 miles and there is a active fire lookout at the top which is pretty neat. Yellowstone is at higher elevation so it will be pretty chilly at night, so come prepared if you will be camping.
The California Science Center in LA has the Space Shuttle Endeavor on display if you are into that kind of thing.
Having done all the cheesy tourist things in SF, I'd recommend Alcatraz Island if you can get tickets. The Ferry Building was also cool. Ride your bikes across the Golden Gate Bridge. Eat at Tonys Pizza Napoletana. Avoid Fisherman's wharf.
Definitely take Highway 1 from LA to SF and I second the suggestion to stop in Big Sur. Some of the most dramatic scenery I've ever seen. And there's a beach in San Luis Obispo that elephant seals like to hang out at!!
You guys are going to have a great time!