I'm a little unclear on what kind of loan you're getting. Is it FHA or conventional? You mention you're "going the Conventional Loan amount of 5% down," but that "repairs adhering to the FHA guidelines." So is this a conventional loan and the lender has told you that they're going to use FHA guidelines?
I also didn't quite follow your numbers, but right off the bat I have a question: is this a renovation loan? Just because you're qualified for a max loan amount of $60k doesn't mean you can just buy the house for $55k and spend the difference ($5k) on repairs. It needs to be a renovation loan that is specifically designed to cover both purchase and renovation costs. The FHA 203k loan is an example of such a loan.
You mentioned that you have been "reading up on what the FHA guidelines are and what they require for a house," but you still have questions. Do you have questions about a specific guideline? What have you found unclear?
Generally speaking, FHA requirements are supposed to ensure the health and habitability of a property. Practically speaking, that means that any safety issues (unsound structural items, unsafe wiring, etc.) and "broken" systems of the house (plumbing, heating, insulation, etc.) will need to be fixed. If the house is broken, you won't be able to just paint it and expect it to pass.
When I last had an FHA 203k inspection done (which was five years ago), I believe the inspection only cost me $350. I'm a little surprised to hear that you're being asked for $1000 up front. You don't need to get the inspection and appraisal together. And does that $1000 cover anything else? If you're unsure about the property, I would get the inspection first and then put down whatever appraisal/application fee the lender is requiring.
And lastly, I have a feeling you're right: $5k is not going to go very far, and even though I don't know a thing about this house, I suspect you're going to need more than that simply because $5k won't pay for much work. You may need to renegotiate your price, or find a better deal.