You neglected the mass-printed fraudulent ballots (more ballots than voters) and violation of voter/ballot thresholds.
That is why I have advocated for the following:
If you choose to vote absentee, you waive your right to a secret ballot. All absentee ballots will be linked by a serial number to the voter, and to the voter's signature envelope.
If there is a successful challenge to the signature matching after the election, the serial number on the signature envelope can be used to find the matching ballot and the votes on the ballot can be removed from the tallies.
No more 'once the ballot is separated from the envelope, there is no way to find it again' excuses. This will limit the ability of someone to 'stuff' the ballot box with faked absentee ballots. Clerks will be required to retain the signature envelopes for inspection by poll watchers and possible legal challenge. The number of signature envelopes on hand must match the number of absentee ballots cast, and the serial numbers must be traceable to having been issued by the Clerk to a valid registered voter (but at this stage not to which specific voter.)
The database of serial numbers will be encrypted and access to it limited to the Clerk and a few full time employees, NO VOLUNTEER ELECTION WORKERS will be able to access this database, and every access will be logged. Only a court order can justify accessing the database. This will limit the exposure of voter's ballots being used for a 'pay to vote a certain way' scheme, and ensure that honest absentee voters will still have reasonable expectation of privacy in their votes.
If you want a strictly secret ballot, vote in person and show photo ID. Ballots cast at a polling place will not be linked to the voter.