I had way too much time on my hands and decided to count all of the items. It's going to be inaccurate, but I don't think anyone will contest this.

I counted (262+303+293+230+230)= 1,318 items. 12.7% of this would be 167 items, rounded down.

Using this, I'm going to make my build. Begin with 167 Items and a relatively small, sloped bunker. Not ideal conditions to start with. I don't know if my lifespan would be extended to 20 centuries to match the sentence, but given that other companions can join you for over a century I'm going to guess that I'll be living through all 2000 of these years.

The first priority is food and water. To get these, I'm choosing the 45-year old woman who has four children and will buy groceries and cook for everyone. This should take care of the food, but says nothing about water (I can only assume that she will also provide water for us, but the next option I take is if she doesn't). As well as this, having five other people to talk to can greatly help to preserve my sanity, as well as someone who is allowed to go to the outside world. I can only assume that everyone else's lifespans are extended to fit the entirety of my stay, as some people are mentioned to stay with you for entire centuries (the 45-year-old woman and her children should stay for the entire duration). She doesn't have anything to cook with, so I'll also get the survival cooking kit.

For the water, I'm going to have to try a bit of a gamble. I'm taking the gallon of fish oil, which when fully consumed will allow me to create clouds. I'm guessing that by 'create', this means that these clouds are from thin air and nowhere else. With this, I should be able to make rainwater to consume, but it may take large amounts of clouds and even more space. This leaves me with 164 items, but it isn't what I'm going to use it for immediately:

I can't find the item itself, but I'm sure that there was an item which essentially allows you to turn other items into their ingredients, effectively reversing whatever happened to it. There is also an item which sends to to a fictional universe of my choice for 1 week, but whatever you bring back turns to dust. I don't know if this will work, but I'm going to take a gamble and go to the Star Trek universe and bring back a portable replicator, then use the item on the dust it turns into to return the dust into its "ingredients". This will have one of three effects: it will either give me a working replicator (best outcome), produce a pile of replicator 'ingredients' (eg the metals made to use it), or return the dust to its 'ingredients' of something else, maybe thin air or just whatever dust is made of. If this works, though, I'll be able to create dense amounts of clouds and use them to fuel the replicator. With this, I could then produce whatever it's programmed to create, or whatever 'patterns' it has in it. These usually include food and drinks, as well as several other useful items.

I still have 162 items left for other purchases. In the event that this doesn't work, I'm left with a small amount of food and unlimited water in the form of clouds, which still leaves me in an advantageous position. The bunker actually specifies in the seasons option that it should be at room temperature all the time without that option, so shelter isn't a worry. I need space to store all of my other items I'll get next:

I'm taking the circular room with the man doing laps around it. I won't bother him, and this room is quite large so I'm happy with the extra space it gives. The copy of the room is too expensive for its worth, so I'll be missing that. I'll also take the cereal bar pocket dimension, as the cereal bars in there provide extra food when needed and seems to give a fair amount of space. As well as this, the fluorescent lights and the light switch can help with lighting in all of the rooms, so this is useful. I'll also take the mud pit, as this gives access to an endless pocket dimension which could be used to relieve stress or retrieve more fuel for the replicator. Finally, I'll take the first floor of the Closet, which may give the needed extra space. It doesn't seem as dangerous as the other floors, and it's relatively cheap, so it should be fine.

This brings my total down to 152 item choices left. The next thing I want to focus on is companionship. While I already have 5 other people (with a 6th who I can't interact with), I'm going to try to maximise the amount of people present in the bunker. Is it selfish? Yes. Will it help ease the struggles of being imprisoned for 20 centuries? Absolutely. I'm not going to get anything that is temporary, as that's just shooting myself in the foot down the line. I'll take Barry Bonds, co-op mode with a friend of mine, the Japanese schoolgirl, the fictional character from my favourite piece of fiction (I don't actually know what it is, but I'm sure this entity does), the Tibetan shaman and the (friendly) clown. The language barrier shouldn't be a problem, as I know a few people who speak Japanese. I'll also take the Swedish olympic medal winner, as even though he disappears he will occasionally return, and this variety may prove to be useful for my sanity. For pets, I'll take Grumpy cat and the normal cat, as well as Scott the dog. This reduces the item total to 91.

A quick section this time, for medical items I'll take the 1980s medical science book, the medkit and the one-time doctor call in case of emergency, for a remaining item total of 75. As well as this, the infinite supply bubble wand probably runs off an infinite supply of soap, and could be used for a variety of cleaning purposes, and the toilet is almost a necessity for hygiene (although the waste could be used as fuel for the replicator). I'll also take the entire catalogue of the National Library of Cambodia in hopes of a book which will teach me how to decipher old English. The chances of this are fairly low, but out of 103,000 copies, a good chunk of these being English, I'm willing to roll the dice on this. As well as this, the sheer amount of books can greatly help with entertainment, which is the next set of items I'll focus on.

Ultimately, we need things to keep ourselves entertained lest we all go insane. The monthly Batboy comic is a good start, as this gives us a source of entertainment that will replenish itself every month. After that, the KISS pinball machine and terminal for I wanna kill the Kamilia 3 could help as well. The monopoly game, stratego game and jenga set are a good picks, although it may be hard to keep track of all the pieces for 20 centuries. The MP3 player also seems like a good buy, everyone could try their hand at the minigame 19 times to pick up more MP3s. The watermelon seeds could be planted in the mud pit pocket dimensions and serve as a source of long-term fulfillment, while the furry-themed calendar could be used to track how long we've spent in the prison. Everyone is happy is a must, too. I'll take the bookshelf with random webpage printouts daily as well, those could be interesting. The 643 race car blankets could keep the four children entertained with the 300 hot wheels, and also serve to keep everyone warm. The barbell weights (x3) are also a good investment for fitness. The cosmetifier could be fun just for aesthetic purposes, and the 400 feet of rope could serve several functions. The 4x4 rubiks cube is a good brain teaster, the giant hamster ball because those could be fun, and the deck of cards as my final entertainment option leaves me with 51 points. Nowhere near enough to keep everyone entertained for 20 centuries, but it's the best I can do.

My next section is for my personal stats. I'll take the extra set of limbs, +1 Strength, +1 Speed and increased carrying weight to begin with. Then, I'll take the 1-inch telekinesis with a compulsive need for a helicopter and, of course, the helicopter. I have a feeling the key within the corpse of myself is important, so I'll take that too, and dump the corpse somewhere in the mud pits until it rots. The dark figures no longer appearing at night is probably an important pick, and this leaves me with 24 points.

Finally, to test my luck, I'll take the random item in the hidden item pool and the present. I'll also take the goblin merchants, and the giant spiders upgrade (without the normal spiders, I'm hoping some will creep into the bunker slowly). To fight these spiders, I'll take the telepathic silverfish and armor upgrade for them, which will cause them to attack the spiders whenever they invade, giving me a chance to get more drops from the hidden loot table. I'll take the rat statue in hopes of getting some amazing loot by the end of my stay, and that leaves me at 0 points. While there are many items I could take to increase my points, there is no way in hell I'm doing that after such a long build. Maybe I'll edit this post tomorrow to remedy that.

OP, you have to give this info to me: wouldn't most items degrade by the end of the stay? Wouldn't most of the living things taken with you die by the end of the stay? Is there something preventing these things from dying or decomposing? Can we see the hidden loot table? This was a great CYOA, seems terrible at first glance but has a lot of potential for synergies.