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Have you talked with your LO to see if you can switch the loan to one of the streamlined type renovation loans so you can complete those specific items after closing?
C5 can be a killer. Technically it's eligible for sale to Fannie Mae (Freddie Mac doesn't purchase C5 or C6 though), but the secondary market doesn't like that rating so it's tough to sell the loan. Freddie Mac doesn't have a 3% down program (only 5% down), Fannie Mae does though. You sure it's Freddie Mac and not Fannie Mae? Even if it was Fannie Mae, a C5 rating still may not be permitted (if deferred maintenance is noted, it almost always needs to be cured prior to closing).
To cure the floors/cabinets, you'll either need to fix them prior to closing or get a rehab loan (FHA 203(k) or Fannie Mae HomeStyle). FHA just requires a 3.5% down payment, HomeStyle will do 5% down. Both down payment %'s are based on the purchase price + cost of rehab combined. FHA does have a maximum loan amount that you may run into though (check your county at https://entp.hud.gov/idapp/html/hicostlook.cfm).