How would you build a pack for such a trip?
What shelter and sleep system would you take?
What would be the best diet? What stove?
Best footwear for first and last 10 days?

Pack - An external frame I think, but might be excessive for the last stage. Maybe the backpack could be partly of wooden and natural fibres, so that you could burn it as fuel once you no longer needed it. Maybe it also serves as shelter.

Shelter - Perhaps a little more focus on comfort than usual, though there wouldn't be as much volume available initially. Hammock maybe. Perhaps a traditional approach where the pack cover is also a tarp, or a hammock. Less volume for sleeping pads than usual, so again a hammock maybe. Perhaps the external frame pack could also be some sort of a cot.

Diet - Over 40 days nutrition becomes more critical, so real balanced food with vitamins and minerals and fibre and stuff. It also needs to be consumable and digestible. Volume is also more of an issue than usual. Some normally good foods are that dense. Perhaps a limited amount of foraging might be permitted also, as long as it doesn't slow you down or take you off your chosen path. Anything it fair game when you make your own rules. I'm an oatmeal fan myself, but for such a trip I think I would throw in stuff like flour and honey and nuts and olive oil. Making bread and stuff can save volume and provide some entertainment. Shelf life becomes a bit of an issue also.

Stove - Kelly Kettle probably, except for making bread. I think I would still bring the Kelly Kettle, and then use the coals from it too start a small fire for making bread in a small pot or pan. Semi-consumables like tin foil might have to give way to something more durable for such a trip.

Light - Hmmm. Solar charging might start to make sense on such a trip. On the last 10 days something for night travel becomes important, but it might not make so much sense to carry extra batteries for 30 days just to have them for the last 10. On the first half of the trip a camp light would be nice, and so you wouldn't think an extra candle or two would hurt, but it might make more sense to go solar electric for all your lighting and communication needs, and save the extra weight for food.

Footwear - I'm thinking a good hiking boot for the first 10 days, and that might work well enough for all 40 days or more since for efficiency you will never be trail running. Towards the end you could go barefoot now and then though. Crocks might be worth it also, depending on ground conditions around camp and the last section of trails.

So the most critical design consideration seems to be the pack system, keeping in mind the varying weight and volume of food carried, and the potential to use the pack material as your shelter system, and perhaps the external frame of the pack could also be a cot?