1. There is a daily bus with multiple daily departures that start from Yosemite Lodge. Reserve/pay for one-way tickets in advance, especially for the early morning (8:00) departure. You have 24 hours to cancel for a full refund. Note: if the buses are full sometimes they will add another bus, so keep checking.
2. Yes, you can park at Glacier Point, but then you get to hike back up there. Also, would have to get up there early in the day else the day-trippers take the spots. Doing the car shuttle is a hassle, plus there will be additional traffic to deal with. (i.e. not recommended)
3. The best part of the loop is between Ottoway Lakes and Washburn Lakes, so suggest spend more time there. Your first day's stop is dependent upon water; often late season many of the smaller creeks along the Illillouette go dry. Your Camp 3 at Triple Peak fork is nice, but if you spend more time on the way over, another nice spot is further down, just above where the Merced Peak Fork meets the trail. Camp 3/Camp 4 are pretty close together. Camp 5 is nice (twin bridges) but another great alternative is to take the upper trail from Echo Valley, climb up, and camp on the huge granite shelf across from Bunnell Point. Great views of the backside of Mt Clark, and there's a small tarn just off the trail. (a filter is preferable for that)
4. Lots of little lakes beyond Red Peak Pass. Suggest making your Camp 3 in that area, and explore it...