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Others have mentioned Jeffs map, it is awesome especially for planning, though I found it less useful on the trip. I brought my copy with me, though I never used it while I was on the trip, I found it to be wayyy too big. I printed a much smaller section of it and laminated it, and I found that to be the perfect map, much smaller and easier to handle than Jeffs but still waterproof/tearproof.

As for your route, as others mentioned it sounds like a lot of time portaging through the woods, as long as you are Ok with that it should be OK, but the poorly maintained trails can be a bit tricky to pass. The portages are usually labeled with yellow signs, the campsites with orange signs, though on my trip there were some portages with no signs and we had to pretty much guess we were on the right trail.

I would also highly recommend 40% DEET bug spray, a bug jacket/net, and if you can, treat your clothes with permethrin before you go! It seems permethrin is a little hard to find in Canada but if you can get it do it (it is available at Walmart in the US and of course online).

There were millions of mosquitoes on my July 8-13 trip, but they visibly were repeled by the permethrin treated clothing. At times I was sitting in the woods surrounded by dozens of mosquitoes, none of which would get close to the clothing, it was quite amazing actually. When I would change into my non treated clothing I was getting bit through it.

The treated clothing worked so well that no joke the mosquitoes were probably one of my favorite parts. There were so many of them you could hear the slight buzzing of millions of mosquito wings echoing across the lakes in the evening. Seriously my fondest memory of the trip was sitting at our island campsite watching the sunset, listening to the slight buzzing sound of millions of mosquitoes.

As for campsites you really should try to stick to the lakes you have permits for, I am not sure of the penalty, but as you mentioned its the busy season so the spot you stay at, even if empty when you get there, is probably going to be taken by someone who does have a permit, which could cause some issues.

I personally found it best to get an exposed campsite, usually I do not like these, but with all the bugs being exposed and having a breeze helped keep them at bay.

Try to do the portages in one trip (ie carry the canoe and your backpack in one trip, taking as many breaks as necessary), this limits how much walking you do overall.

Well... I'll get you started. As you're new to this, please ask lots and lots of questions.

Temperature in late September: it can range from 8-20 C during the day. For the most part, it'll be around 0-2 C overnight, but you might run into a -5C night.

There is access to the Highlands trail from the back of the Mew Lake campground. However, in the fall (I'm not sure of the exact date), I believe that you have to check in at the West Gate for the Highlands. But, either way, don't worry - your bus will stop at the West Gate.

For Western Uplands, you definitely have to check in at the West Gate year-round. From there, its a 3km walk up the road to the Oxtongue River Picnic Area which is also the trailhead for Western Uplands. You may also be able to hitch a ride from the West Gate.

There are next to no bugs in the fall.

The lakes will be cool. Certainly, some brave souls do swim. Personally, its a bit cold for me.

Yes, Algonquin does have both black bears and wolves. It'll be unlikely that you see one, and extremely unlikely that one will pursue you. However, make sure to hang your food, dishes, and toiletries as night about 200' from your tent.

Water is abundant throughout Algonquin. I doubt you could hike more than an hour without crossing a lake or stream. Of course, like everywhere, there are viruses and bacteria - so, make sure to boil, chemically treat, or filter your water. Personally, I use a Sawyer Squeeze and also bring backup Aquatabs in my med kit - but there are lots of choices available.

Is it safe for a solo female? For the most part - 99.9% - yes. I've never heard of any harassment in the Algonquin backcountry.

In the fall, I would not expect to see a lot of people on the trail. Probably 1-3 groups of hikers each day. The campsites are fairly secluded, so there won't be anyone around at night.

As for cell phone reception: there is reception along the highway, but expect none on the backpacking trails.

This is why I keep mine in a watertight container (with my electronic car key) and inside a dry bag.

Failing this can be tricky, specially if you are the one driving others home, like I am.

Imagine, dead car key (fob controls push button ignition) in the middle of Algonquin, no phone and your rather irate com-padres, staring down at the idiot who forgot to protect his shit leaving them stranded in the middle of nowhere...

Makes you wonder if anyone picks up hitchhikers on rural roads in those woods?