Finally i have free time to read your thesis. My comment, thoughts & question :
1. On 1 - Introduction. You forget to mention 2 proposals (which published before date before of your thesis) which aim to improve anonymity which are BIP 151 and 156, even though it's not anonymization by modify transaction.
2. Upcoming bitcoin proposal, Schnorr MuSig could improve privacy on transaction with multiple input, you might be interested.
3. On 2.3 Privacy in Bitcoin. You should take not that :

• Few wallet such as Electrum now randomize output order
• Few wallet have multiple change address feature
• Few wallet such as Samourai wallet have advance transaction generation to improve user's privacy. It's called Stonewall

4. Your attempt to de-anonymize coinmixer.se is great, especially distinguish customer/coinmixer address by "Following transaction fulfills fee indicator", "Received an uncommon value" and "Tx fee based on partitions correct"
5. Why did you use blockchain.info rather than use Bitcoin Core RPC-JSON?

More info :
1. BIP 151 : Peer-to-Peer Communication Encryption
2. BIP 156 : Dandelion - Privacy Enhancing Routing
3. Dandelion: Redesigning the Bitcoin Network for Anonymity
4. Dandelion++: Lightweight Cryptocurrency Networking with Formal Anonymity Guarantees
5. MuSig: Schnorr Multisig and signature aggregation
5. Samourai Wallet : Stonewall

Although I think .io is owned by ChipMixer too, .com is the official domain: Please use the correct URL in all your posts: