Hi Scott,
You will likely have some issues with this property requiring repair. They want you to purchase a home in move-in ready condition and one that is safe, structurally sound and sanitary. It sounds like you've reviewed the VA's MPRs but know that the appraiser also has a lot of discretion when it comes to determining which repairs will be required to ensure the home meets the 3 S's.
As the buyer you have multiple options:
1. Negotiate up front with the seller to have them complete the repairs before the appraiser even comes out.
2. Wait and see what repairs are going to be required and then negotiate with the seller or pay for them out of pocket. If you are going to pay for them out of pocket, protect yourself as much as possible by getting your loan CTC other than the repair requirements, etc. Talk this through with your lender to figure out the best course of action.
3. Find another home that is in move-in ready condition
4. select another loan type that may have less stringent standards.
Another thing to note when budgeting is that you will pay the initial appraisal fee (between $300 - $500 depending on your state) and then you will have an additional reinspection fee of $100 when the appraiser goes back out to the property to inspect and confirm the repairs are complete and correct.
Hope that helps,
Samantha