Hello, my name is***** and I have over 20 years of experience as a veterinarian. I'm really sorry to hear about Thomas's strange behavior including confining himself to your room, sleeping only on the furniture, not using the litterbox and excessive scratching.
The most likely reason for these symptoms is flea allergy dermatitis.
Thomas may be associating leaving the furniture in your room with flea bites, and isn't willing to leave your room and possibly get bit going to the litter box.
Flea allergy dermatitis is horrible. If you only see a few fleas on him you might have a huge population in the environment/floors. In allergic cats there doesn't need to be many fleas to feel the effects, it only takes one bite a month for an allergic cat to itch like crazy. If you have other pets who aren't itchy they may not be allergic. Ideally I recommend topical flea products be applied every 3 weeks on an allergic cat when fleas are at their peak, or with a active problem and then monthly as a prevention. Many over the counter products have a problem with fleas being resistant and some can be down right dangerous. I never recommend any products that Hartz or Sargent's make. I recommend Advantage II or Frontline Plus, or the new Seresto Flea collar. I don't normally recommend flea collars, but this one really works and lasts for at least 6-8 months. All pets in the house must be treated as if you don't the nonallergic ones serve as a flea reservoir for the allergic one and you'll never solve your problem.
It is important to realize that only 5% of the flea population lives on your cat, the rest is in the environment.
You need to vacuum your home throughly to remove as many eggs and larvae as possible. Concentrate on cracks and crevices, along baseboards, under furniture and areas where they like to sleep and eggs and larvae are at their highest numbers. Vacuum daily and throw away the bag.
You also need to use effective products on your cat as I outlined above.
I also recommend treating the home environment with a product that has an adulticide (kills adult fleas) as well as an insect growth regulator to stop egg and larvae from developing. A great product is Siphotrol II Plus Premise spray. I like it because it has an insect growth regulator as well as an adulticide. You can spray it under furniture and into cracks crevices and along baseboards where fleas and their offspring hide. It should be used every 2 weeks and no vacuuming for 2 to 3 days after using it to allow it to settle in. Here is a link to show you the product: http://www.amazon.com/Siphotrol-Plus-Premise-Spray-16oz/dp/B000RGKX7M
The trouble with foggers is that they don't go under furniture or penetrate cracks and crevices so they just aren't effective where they need to be. And they end up in the air where they are nasal irritants for animals and people alike.
Your other option is to have a professional exterminator treat your home and outdoors if Thomas goes outside. Ask for a guarantee and make sure that the products they use don't contain organophosphates and do have an adulticide and an insect growth regulator.
The key with flea treatment is consistency, not stopping too quickly, and using effective products.
To control allergic symptoms in the meantime you can give Thomas:
1) Benadryl (diphenhydramine only, the combination products with decongestants and acetaminophen are toxic to cats) at 1mg to 2mg per pound every 8 hours. That's a half of 25mg tablet every 8 hours for a cat that is 8 to 15 pounds.
2) Chlorpheniramine at 4mg twice daily.
3) Zyrtec (Cetirizine hydrochloride) at a dose of 5 mg per cat given orally every 24 hours. Make sure it is NOT the formulation with a decongestant (such as Zyrtec-D) because cats cannot tolerate decongestants.
Combined with high doses of omega-3 fatty acids antihistamines work to relieve her itchiness. I like 3V caps or Derm Caps as they are reputable, high quality products. I recommend a dose based upon the EPA portion (eicosapentanoic acid) of the supplement as if we do that the rest of the supplement will be properly balanced. Give him 20mg of EPA per pound of body weight per day. For example an 8 pound cat could take 160mg of EPA per day. Antihistamines and omega-3 fatty acids work synergistically, better together than either one alone. These should help reduce the itch. Be aware that antihistamines can cause drowsiness or hyperactivity which should resolve with continued use.
If there are other cats in the home that he doesn't get along with or outdoors that upset him perhaps part of this is stress related. If so a product called Feliway, which is a synthetic version of a calming feline pheromone, may help. You can purchase this from petstores or online.
It is possible too for fleas to pass on diseases when they bite which could make Thomas feel poorly, such as a Mycoplasma infection. So if he is eating poorly and sleeping all the time a veterinary visit to make sure he is healthy is best.
For now I would start with flea control on all pets and in your home, an antihistamine and omega 3 fatty acids. If he's not significantly better in 2 weeks then it's time for a veterinary examination to look further for problems.
It may help to put a litter box in your room for now so that he has quick access to one until the flea situation is sorted out.
Please let me know if you have further questions by replying to this post.