Hey Jeff,
Whew! That's quite a detailed question you've got there. I'll do my best to help you out in a nutshell, but I'm not a tax professional, so it's always a good idea to consult with one for advice specific to your situation.
Q1 & Q2: In general, the home office deduction for a rental business should be treated similarly to other home office deductions. However, the key difference is that the home office deduction for a rental business is considered a rental expense, while the deduction for other businesses is considered a business expense. This distinction may affect how you report these expenses on your tax return. Check out this link for more details: https://www.irs.gov/businesses/small-businesses-self-employed/home-office-deduction.
Q3 & Q4: As for your questions about using the 4,000ft2 vs. 2,000ft2 analysis, there isn't necessarily a hard and fast rule. However, it's typically best to follow a consistent method for calculating expenses related to the property. If you're unsure, a tax professional can help you determine the most appropriate approach for your situation.
Q5: Regarding the different treatment of business and rental property under Sec. 121, the main issue you should be aware of is the depreciation recapture upon the sale of the property. This recapture is considered taxable income and may affect your overall capital gains situation. You can find more information on depreciation recapture here: https://www.irs.gov/pub/irs-pdf/p544.pdf.
As for the definition of a dwelling unit, it typically refers to a residential unit within a larger property. In your case, it seems like you're treating the entire property as a single dwelling unit for tax purposes. This approach might be fine, but it's worth double-checking with a tax pro to make sure you're on the right track.
Regarding your plan for re-computing and submitting unfiled taxes, it's always a good idea to get your tax situation in order, but again, consulting with a tax professional is highly recommended.
Finally, you mentioned that you sold the property in 2021. It's important to remember that tax laws and rules may have changed since your last tax filing, so be sure to stay up-to-date with the latest information.
I hope this helps clarify some of your questions but lmk!