If our agent pays him via checks and bills us at closing, does this have any +ve or -ve impact on the taxes? 

When we were the lender we would foreclose on the property or have the HOA buyer pay us off.

This means instead of getting a mortgage from the bank, you pay the seller in installments.

And we pay them direct from rehab draws on my loans.6.

My market is seasonal and I was begging for enough revenue just to cover my mortgage so I wouldn't have to pay my own rent AND a mortgage. 

Not sure if it is worth it to just pay them out or proceed with evictions. 

The difference is that on the 2k house you can pay for that HVAC relatively quickly, where as the 800 house it takes many months to offset the costs.The same can be said for other costs such as property management. 

I dont think you need advice for anyone how to structure this your already experienced operator.. the decisions is do you want to keep adding doors or concentrate on paying off what you have.

I would get an engineer in there, get a quote on the work, and try to negotiate the seller to pay to get the work done

The SFH and the 1b/1ba ADU are currently occupied by tenants under RSO and paying far below market rents.