Andrew covered most of the bases very well–I’ll just supplement his thoughts with another voice.
I will probably be in the vicinity of Rae Lakes loop this weekend, also starting Friday AM at the Copper Creek Trailhead, ascending Granite Pass, intersecting the JMT, ascending Mather and Pinchot Passes, then intersecting Rae Lakes Loop at Wood’s Creek crossing, and completing CW Rae Lakes loop from there (see here). So I’ve been looking at weather, etc for the region. It’s aggressive, but I plan to do that in three days.
1) I’ve done the Rae Lakes loop twice, once in 6 days (with my wife, adding 60 Lake Basin–first backpacking trip; I had a 55 lb pack!), once in 4 days (with my dad, adding 60 Lake Basin). If I were to do the loop solo this weekend, I’d do it in two days. Three days is eminently doable. If I were to do it in three days, I’d probably spend the first night at Upper Paradise Valley (assuming CW), second night at Rae Lakes or in Sixty Lake basin (a worthwhile addition), and go over Glen and finish on the third day. If going CCW, I’d probably add a detour to East Lake, and camp the first night at East Lake, second at Wood’s Creek crossing.
2) Get there early, but I think your prospects are good, especially if you’re willing to go CCW (Bubb’s Creek).
3) Mosquitos should be pretty tame–you’ll probably see a few, but that’s it. I would recommend (and am) leaving netting and DEET at home. Bears are active on Rae Lakes loop. I’ve seen them both times I’ve done it. You’ll need a bear canister for food storage. I think they can be rented from Road’s End.
4) It’s a very wet loop, as Andrew pointed out. But while there is plenty of water available, there are no stream crossings of note.
5) If you want the bigger climbs first, go CCW (Bubb’s Creek). This is typically the easier permit to get. The loop is essentially up up up down down down, so no matter which way you go, it will be an easy finish. Most prefer going CW to acclimate a bit before going over Glen Pass.
6) I see the same thing Andrew does, from weather.gov. I’ll look at it Thursday, to better know what to anticipate. As usual, I anticipate afternoon thunderstorms in the Sierra. Extended storms happen, but are rare–the forecast doesn’t show that as likely as of now. As Andrew pointed out, try to clear the high passes early in the day if thunderstorm activity appears likely.
7) No comment – haven’t fished on the loop
8) Absolutely not. If you were worried about needing crampons on Island Pass, I’m surprised you didn’t ask about them on Glen Pass. Island Pass is barely a pass. The first time I went over it, I didn’t even realize I had gone over a pass. Regardless–in both cases, you absolutely don’t need crampons.