1) generally, shouldn't be a problem.  Leave yourself a bit of leeway (which stopping at 2 pm would certainly do) to allow for moving on to the next campsite if the one you are planning on is taken (happened once in two weeks to us).  I did the Allagash trip in 1982, so things may be a bit different now, but the only place that seemed "crowded" was up in Allagash Lake (we went upstream to the lake from Chamberlain Lake, spent a couple of days there, and then came back down river to Chamberlain and on to Allagash Village.  Campsites are similar to BWCA, but "deluxe" version with picnic tables, fire rings and nice outhouses.  Picnic tables have a ridgepole over them so you can rig a tarp over the table.  If you haven't already done so, contact whoever it is in Maine that runs the Allagash and request a copy of the river map - it shows the locations of all the campsites.  I can't recall if you are required to camp in the designated sites, but I think that is so.  If you wind up on the same "schedule" as another group, you may have to leapfrog them for campsites, otherwise, you should have plenty of options.

2) probably safe enough, though I used Iodine tablets on that trip - realize that the "Wilderness Waterway" is a very narrow strip of land bordering the lakes and river - everything outside the waterway is private timberland, so there could be anything in the streams that feed into the system - not saying there is a problem, just that there could be, so I'd filter - regardless, the lakes and river appear pristeen.

3) about as likely as anywhere else - there is always wind, and the later in the day it gets, the stronger it blows, but unless there is a strom front moving through, you shouldn't get wind bound.

4) we spent two nights at Allagash Falls - we did the trip the first two weeks in June, taking our time, which is why we did the up and back detour to Allagash Lake.  At that time, there were a bunch of Kokanee salmon that had run upriver to the falls, and fishing was pretty good there - just threw in floating rapalas, and twitched em a bit as they floated down the current.  It was not a zoo atmosphere, and probably only a couple of parties went past us.

5) can't remember, but they all seemed pretty nice;  I'm heading out to Q this Friday - when I get back, I'll look up my trip and see if I had any notes on any campsites.  

Do take time to go and look the old Locomotives -

fishing was for big brookies and lakers in the lakes, trolling, and fishing the rapids for smaller brookies was good.

You will likely have low water conditions unless you luck out with a lot of rain at the right time-  bring Royalex, not Kevlar (we used our Grumman with no problem, though we did hang up once on a rock in Chase) - the lower section of the river will be a challenge to find the deeper channels between gravel bars; Chase Rapids (CII) will be bony - hope you have good whitewater skills - do a lot of backpaddling to slow down and pick your route through the rocks - 8 miles of rapid, woo hoo!.  The ranger on duty at the dam opend the floodgates every morning, about 6 or 7 am - that is when you want to hit that section, a bit after the water comes up (you'll hear him running a chain saw to work the gates - you can/should arrange for the ranger to shuttle your gear to a spot below the first/harder section of rapids - easier to manouver a lighter canoe, and you won't rishk any gear that way, other than your boat.

Supposedly, the number of users on the "Gash" has fallen off in recent years, so I don't think it will be too crowded for you, even though you are going in peak summer season.  We saw Moose most every day, probably something like 30 to 40 Moose on the whole trip, all along the river.

I'd suggest camping near the dam if you have a layover day available, and using the layover to fish and scout the rapids - we caught a lot of brookies in there, and it gives you a bit of a chance to see what the rapids are like.  Used spinner/worm combo for fishing the rapids

Ther are 2 or 3 ? portages, all easy hikes.

NPMB is a good website to ask other questions, if you want more current info.

Great trip - I will go back and do it again someday.