@Justin McElroy  I think most lenders who will be financing construction costs along with the purchase will need contractor bids as part of the loan application, and you may need approved building permits before closing. 

Bedroom will be unfurnished but rest of shared space will be furnished.1. can I claim 50% of cost on furnishings and applicances?

It will take you to a screen where you enter the applicable information.

The application was initially conventional 

I'd write him a personal letter, and send a copy of it to the bank where  you probably paid the appraisal fee to saying that the services he rendered were incomplete, unsatisfactory and need to be disqualified from your mortgage application and you want the bank to reassign a different appraise to do the work.You can sight the discrepancies.I think appraisers are registered and have to keep up their credentials I'd send a copy of the letter to whom ever they get their accreditation from to let them know how unsatisfied you were with the service, if you get no help from the bank. 

Simultaneous Second Home or Investment Property TransactionsIf a lender is processing multiple second home or investment property applications simultaneously, the same assets may be used to satisfy the reserve requirements for both mortgage applications.

To share some numbers on how many projects are being submitted with multiple units... see below data on the permit applications for City of San Diego, which is a combo of public data + our analysis on text fields describing the projects (to extract things like unit counts... it's directional, not perfect data).

However, receiving section 8 rent portion may still be applicable here. 

They are welcome to submit a complete application if they wish to remain and sign a new agreement with our terms, which may, or may not, be different from current terms, depending on our findings of condition, current market conditions, and their credit worthiness.Be sure you are getting the security deposits transferred to you at closing, and confirmation of rents/deposit with estoppel.

I discuss all of these topics at application and interview for the apartment because if they have an issue with any of those items we never make it to lease signing anyway.