if you're a contractor, you can clean up. most people have no idea what they're buying - you will. and you can renovate cheap.
a 5% down conventional loan will mean you'll be paying for private mortgage insurance. which is expensive. if you can put the 20% down, do it. if you need to go with less, just pay off the principle as fast as you can till you hit 20% (you don't need pmi after 20%). on the fha low down payment loans, i think they go as low as 3% down, but you're still paying for mortgage insurance (not private, might be a little cheaper, but you're still paying).
shop around a lot for your loan. the terms and costs vary a lot. i got mine through costco's screening thing, and the discount was substantially more than the membership fee. the bank i used was in the kc area. they were ok to deal with and (obviously) the lowest price i found for the loan i wanted. kinda mumped me over on rate lock fees when my closing was delayed. i expect other banks would have done the same though. anyways, capwest mortgage.