Cottered cranks can be a bear. Start soaking the bolts at the threads in Liquid Wrench now. Might as well soak other bolts that are coming out too. When you put the bike back together, use a plastic bottom bracket sleeve to keep gunk out of the bearings.
On that note, replace the bearings in the headset, front hub and bottom bracket. I would use loose balls instead of cages, which is probably what you have in the headset and BB.
Don't forget to treat the inside of the frame with Framesaver!