Wow what a fun trip! Quick question- is this a trip for adults or a family with kids? Here are some general suggestions or answers to your questions. Keep in mind June will be very crowded in Yosemite, the valley will be packed during the day. The waterfalls will probably be pretty weak this year due to the lack of rain/snow, but since it is early summer hopefully they won't be too bad yet- I'll cross my fingers for you!
Here's what I got so far for a June trip:
Sunday - Yosemite National Park (Tenaya Lodge at Fish Camp)-
Tenaya Lodge is beautiful, but make sure you plan enough time each day to drive in to valley as it is windy and slow.
Mon - Park (Yosemite Falls, hotel hop, rent bikes, go commando on Yosemite)-
I am not sure what you mean by hotel hop, there is only one hotel to see in the valley (The Ahwanee), and yes it is beautiful (like the Wilderness lodge, but with a better view outside- if you plan to eat there you need to be dressed up!). Bikes are a great way to get around the valley on the main paths. Keep in mind it is best to pack a lunch with you. There are not really any good places to eat in the valley. My favorite waterfall is Vernal Falls, but it is a pretty long hike up to it (so consider your hiking level and alloted time first). Yosemite Falls you can see from numerous spots in the valley. There is a free shuttle that runs through the valley and stops at all of the main tourist spots, so I don't see the need for a bus tour. There is a little museum in the main village area by yosemite falls that if you have kids you can walk them through and there is a nice Ansel Adams gift shop.
Tues - Park/Mariposa for the trees-
lf you are wanting to see the other hotel since you mentioned hotel hopping, this would be the time to see the Wawona since it is close by. You can park in the parking lot at the mini mart/gas station and the hotel and a small museum is just right there that you can walk through. The Wawona is pretty, but it is not really a hotel with a big lobby that you can explore or anything. From this parking lot you can take a shuttle over to Mariposa grove if their lot is already full. Two hikes in upper yosemite that are wonderful are Taft Point and Sentinel Dome. Sentinel Dome has amazing view and both hikes are right next to each other and they are very short and easy (you could do both pretty quickly). When you reach Sentinel Dome though you have to climb around on the giant rock for the view so if you have kids be careful...we with kids you have to be careful everywhere there. The views will not disappoint on either of these hikes.
Wed - Glacier Point and travel to Monterey (hotel undecided but want something on ocean) How long will it take to reach monterey? How are the roads out of yosemite?-
how are the roads...windy! If you get car sick be prepared, but the drive is pretty. If you want a hotel on the ocean, be prepared to pay a pretty penny and make sure you are getting one near the sights in Monterey. Some say on the water, but are not near the main area of Monterey. The Monterey Plaza hotel is on the bay and is very beautiful- but very expensive.
Thursday - Monterey Aquarium-
so fun, you'll have a blast!
Friday - 17 mile drive, Pebble Beach, Big Sur-
I can't believe I haven't been to Big Sur! We were supposed to go last summer, but everything was on fire Hope you have a great time there, make sure to visit the waterfall at Julia Pfieffer state park I hear it's beautiful.
Sat - Nothing but ocean and relaxation-
are you planning to drive to SF this day? There are beautiful beaches everywhere, the ones along the 17 mile drive are nice, and Carmel has some beautiful ones too.
Sun - San Fran (pier, cable cars, golden gate bridge)-
wow this is a lot to cram into one day, the wait for the cable cars alone can take forever. There is sooo much to see here and it is a really big city. If you have never been before, make sure you look around and decide what you really want to see and what you can save for another trip.
Mon - head home
Good Luck with your planning, hopefully something on here helped you. You can read my Monterey trip report in my siggie if you want some other ideas for there. Otherwise- have fun! Be prepared for lots of driving!