CTR aggregation rules state that a CTR is required if more than $10,000 in cash in deposited by or on behalf of a single entity. In your first example, more than $10,000 was deposited on behalf of John Doe. Consequently you have three part I's.
John Doe - box 2c transactions conducted on his behalf. Also check Multiple transactions since there were two deposits to his accounts. List $11,000 for John and both accounts.
John's son - box 2b transactions conducted on behalf of another. Do not check multiple transactions. He only made one deposit. Only list the D/B/A account and $7,000 for junior.
Jane - box 2a transactions conducted on own behalf since she is an owner of the joint account. Do not check multiple transactions. Only list the joint account and $4,000.
Second example. These transactions must be aggregated since they were performed by the same person. There will be 4 part I's. Yogi - box 2b transactions conducted on behalf of another (the three LLCs). Check box 3 since there were three deposits. List all accounts and $12,000.00
For each LLC - box 2c transactions conducted on their behalf. Do not check box 3 since they each only had one transaction. List only the LLCs account number and appropriate dollar amount of the deposit for each.
John & Ken, I passed my CAMS this month. Did I get this test question right, too?