I've been on the Middle Fork multiple times in August at some of the lowest levels imaginable.
Depending upon snow pack and rain over the summer, it's possible / probable that the upper 25 miles, from Boundary Creek to Pistol Creek will be super low and the hardest portion of the trip. To me, this is also the most interesting part of the trip, so I always try to make sure to launch from the top (Boundary Creek) regardless of the flow instead of flying into Indian Creek.
If the commercials are still running sweep rafts off the top, you'll be able to make it down in a self-supported kayak. Four options you might want to consider:
1) You can carry more / get across more shallow water / hop in and out of an inflatable kayak easier than a regular kayak. For self-supported trips, we often have each person paddling a tandem inflatable to allow a much more comfortable trip than what fits in our regular kayaks.
2) You can also lighten the load by going super light up top and flying additional supplies into Indian Creek, Stateland, Loon Creek, or Flying B. Sometimes, if you ask super nice and/or bribe with beer / bourbon / etc, you can get the commercials to add a bag to one of their fly-ins (when the water is low, they fly their guests into Indian Creek and dead-head the rafts from the top).
3) If money is no object, look into renting a cabin / bed at Loon Creek and/or Flying B. Both have showers and will provide a hot supper, hot breakfast, and bag lunch for the next day. You can also do layover days there by paying for 2 nights. It's not cheap, but it allows you to substantially reduce what you need to carry and makes an easier trip for those not use to doing a minimal kayak self-supported trip.
4) If it's just the two of you, take all 8 days that you can get for a small trip. Plan small days up top, especially the first day. When we're running small late season trips, we often try to get Trail Flat hot springs at mile 6.9 as our first camp. Sometimes we only then run down to Sheepeater hot springs at mile 13 for our second camp. And Dolly Lake / Big Snag at mile 19 / 19.1 for our third camp. Technically, you're only allowed one hot springs camp, but when the water is low the rangers move to Indian Creek airstrip, and one can occasionally finesse that rule (particularly if one's trip is one or two people and you share the site). Below Pistol Creek (mile 21.4) the river opens up a bit and you can paddle in a straight line and make more miles (even though the water is slower).
The Middle Fork of the Salmon is, bar none, my favorite river trip. I've run it 40+ times from late April into early September and have always had a great time. It's wilderness, so it can throw surprises at you, but that's part of what makes it unique. I've run everything from a solo self-supported Perception Pirouette to a solo 16 foot paddle raft with my 70 year old Mom and a 100 pound dog off the top, both of those in late August at ultra low flows, so I totally believe you'll be able to run off the top self-supporting in August / September.
Have a great trip!
reinharden