The 90-day flip rule is a secondary concern. Your primary concern is any health & safety issues that might cause you physical harm or prevent your FHA financing. When an FHA appraisal is performed on a home, the appraiser is really only looking safety hazards and that the house is structurally sound.
In various areas of the FHA Appraiser's Handbook there is clear direction to have the Appraiser note safety/hazards for repair. For example:
"Required repairs are limited to those repairs necessary to preserve the continued marketability of the property and to protect the health and safety of the occupants."
"The property must be free of all known hazards and adverse conditions that: may affect the health and safety of the occupants.."
"The appraiser must note and make a repair requirement for any health or safety deficiencies as they relate to the subject property,.."
What actually constitutes a "health & safety" issue was revisited in a 2005 Mortgagee Letter (this is how FHA changes/clarifications are announced). There are many examples of items that DO and DO NOT fall under the category of a "health & safety" issue. http://docs.steven-anthony.com/ML05-48-Repair-InspAppraisalP
If there's something that comes up during your inspections that you'd like to have repaired, you can simply request those repairs to be done. The seller isn't necessarily going to complete any or all of them, but you can certainly ask, or request credit for them. Good luck!
Repairs don't have to be done if they are found in the inspection. However some of them maybe required to be fixed by the lender if they are called out during the appraisal. It all depends on the lender and their under writer. The home inspection is for your peace of mind and gives you the knowledge to make an sound purchase. If there are repairs in the report that you feel need to be fixed, you can have your agent request for them to be repaired.