@John Pu
I'll try to answer some of your questions here.
1) Due diligence should involve verifying all the numbers as on any deal, structural inspections, environmental study, etc. You should also be looking at demographics, traffic patterns, and of course getting bids on the cost of rehab. Visit the city and ask about what sorts of uses the zoning allows and if there are any current known violations or "grandfathering". If you are using a broker, they should be able to help you through all of this.
2) NNN property typically is offered at a lesser cap rate because it's considered a more stable long term investment than a residential multi family. Leases are usually 5+ years and have built in rate hikes of 3-5%/year and expenses get passed direct to the tenants via NNN. There are pluses and minuses to having a big chain anchor.
3) This is not something I have experience with so I will leave it to an expert in that space.
4) There are some great advantages to owner financing IMO. First off, there are no loan points or closing costs associated with the loan. There's also no appraisal required. The owner might be more flexible on rates and terms than a typical commercial lender will be. The owner financed deal can also close far quicker than with bank financing. If the property needs work, this makes even more sense since the bank might take a look at the project and either decide they don't want to do the loan at all or they will only give you a 65% LTV because of the perceived risk. Use the owner as the bank, then get the property rehabbed and fully stabilized. Then refi back up to a 70-75% LTV based on the new value you have created.
Quick note about the drawbacks of a big name chain... They will typically come in and try to take control away from you. I don't mean they will come in and want to run your property for you. But they will come in and try to grind you on many, many aspects of your deal. They will dictate your tenant mix by putting language in your lease restricting other tenants you can rent to. They will want a better rate on their lease because they know that they add value to your property just by being there. Also, these sorts of tenants can take a LONG time to make decisions and sign leases.