* Who gets the txn fees that are put on small txns? I sent a small txn to another wallet of my own, and was charged a small fee. Who got that fee? I did not get it, and nobody else took part in the txn! Where did that money go? Who got that money?
The miner who processed your transaction got the transaction fee.
* How is balance within a coin tracked? - The transaction list is a clear concept as I presented it, but I present it as if the bitcoin were an atom which is not true. How is subdivision of a bitcoin handled? The balance and the ownership of each fraction will need to be tracked and checked for each txn and if there are many small ones they would be scattered all along the block chain which would make validating a single txn inefficient.
A "bitcoin" is defined as 100,000,000 base units. Ownership (the right to transfer the base units) is tracked by the transactions.
* selfish blocks - A node could pretend to receive no other txns except its own txn 0, and simply focus on hashing. This would be an unfair an advantage, though a small one. Sounds feasible but not scary.
I'm not sure what you mean. Miners are not obligated to include any transactions and it does happen that they only include transactions that have a fee.
* Takeover the irc server and direct all new peers to a darknet of their own controlled nodes so they can establish their own dominant block chain.
This is only an issue with the mainline client. Additionally, you'd still have to create blocks with the current difficulty which is quite hard.