If a business owner makes a large deposit into the business account, how many Part 1s are completed on the CTR? One for the business as 2c, one for the person conducting the transaction for another as 2b, and one for the person conducting transaction on own behalf as 2a since they are the owner? So 3 Part 1s?

I would only do two part 1s...one for the business and one for the person conducting the transaction for another.

The answer depends on how the business is owned. Is it a corporation, partnership, LLC, sole proprietor, etc.?

In this specific case, the business is a corporation.

In a case where it is a personal account and there are two joint account holders and one of the account holders makes a deposit into the account, would there be a Part 1 as a 2a for the joint holder making the deposit and conducting the transaction on their own behalf, a 2b for the same joint holder conducting the transaction for another (the second joint holder), and then a 2c for the second joint account holder?

Then SmallBankBSA's answer is correct. Owners and signers or corporations are not included on CTRs as having deposits done on their behalf. It is the entity whose behalf the deposit is made on. See the April 2018 FinCEN beneficial owner FAQs

Question 33: Listing beneficiaries on CTRs

When completing a CTR for a business (i.e., corporations, limited liability companies, and general partnerships) will beneficial owners now need to be listed as beneficiaries in such CTRs? If yes, would this also include trust and estate accounts?

A. No. The Rule does not change the existing currency transaction reporting requirements or any guidance FinCEN published pursuant to this reporting requirement. Thus, a covered financial institution is not required to list the beneficial owners of a business, or trust or estate account, when completing a CTR as a matter of course. A financial institution must list a beneficial owner in Part 1 of the CTR only if the financial institution has knowledge that the transaction(s) requiring the filing is made on behalf of the beneficial owner and results in either cash in or cash out totaling more than $10,000 during any one business day.

Not that anyone asked, but if the scenario involved a business account where the business is a sole proprietorship, and the owner of the business is making the deposit, there is only one Part 1, and it's for the owner, with box 2a (on own behalf) checked.

CTR FAQ #23 answers your second question.

23. How do I properly complete Part I on the FinCEN CTR for deposits into a joint account? What amounts do we show in Item 21 for each Part I? For example, John and Jane Smith have a joint account together. John Smith deposited $5,000 into the…
How do I properly complete Part I on the FinCEN CTR for deposits into a joint account? What amounts do we show in Item 21 for each Part I? For example, John and Jane Smith have a joint account together. John Smith deposited $5,000 into the account; later in the same business day, Jane Smith deposited $7,000 into the account.

When a deposit is made into a joint account, the deposit is presumed to be made on the behalf of all account holders because all account holders have potential access to the account balance, and multiple Part Is are required. In this example, the financial institution would complete four Part Is, two for John Smith and two for Jane Smith since each person has more than one Item 2 role.

One of the Part Is for John Smith would be completed by checking 2a "Person conducting transaction on own behalf" and entering $5,000 into Item 21 and the account number of the joint account. The other Part I for John Smith would be completed by checking 2c "Person on whose behalf transaction was conducted" and entering $7,000 into Item 21 and the account number of the joint account. One of the Part Is for Jane Smith would be completed by checking 2a "Person conducting transaction on own behalf" and entering $7,000 into Item 21 and the account number of the joint account. The other Part I for Jane would be completed by checking 2c "Person on whose behalf transaction was conducted" and entering $5,000 into Item 21 and the account number of the joint account.

Note: If Jane Smith did not conduct a deposit, but John Smith deposited $12,000 into the joint account, there would only be two Part Is. One Part I would be for John Smith as 2a "Person conducting transaction on own behalf" and entering $12,000 in Item 21 and the account number affected. The other Part I would be for Jane smith, checking 2c "Person on whose behalf transaction was conducted," entering $12,000 in Item 21, and providing the account number affected.

In your example, only one joint owner made a deposit so there would only be two Part I's as noted above. If both joint owners made deposits, there would be four Part I's.

Thank you everyone who responded. Your answers will be helpful going forward.