first a disclaimer: this is how I did it thirty years ago with the boyscouts about a half dozen times. Definately register and post on the NWPMP for a more current plan.
Camp your first night at least 1/2 down Seboomook lake. Although this lake gets its share of wind it usually funnels down the lake. Get up at sunrise and out on the water early! It's not the distance that will get you but the time element. When you approach the dam portage around the left side and follow the trail down the hill just below a rocky rapid at the base of the dam. Paddle a short distance, around a few bends and portage left around a double ledge drop. Paddle a 1/2 mile-3/4 miles and listen for the roar of major rapids. Portage all your gear for one mile down a portage trail on your right. At the end of trails is/was the roll dam campsite where the trail ends and where the road meets the river. Stash your gear in the woods while you hike back up the portage trail. On the way back up the trail scout/view the rapids. Portage your canoes down the first 1/2 of the portage trail. The lower set of ledges are the ones typically done in open canoes that are empty. You should have a basic knowledge of running ledge drops, bracing, and using a throw rope if you attempt this lower section. Do not attempt the first set of ledges, they are more difficult and dangerous. If you are unsure about even trying whitewater you should portage the 2.5 on the road, it should be wheelable. My way the total portaging is probably less than 1.3 miles one way but it is rocky and has roots- no wheels but you can see many of the rapids and if you want to try running them you can. Good luck. PS the blackflies are horrendous at roll dam in May/June.