Kerry,
Depends on what you want out of the loan. If I understand you correctly you own the home outright currently and your son lives there. Some quick answers for you....
1. This would not be commercial. Commercial is only for 5 or more units. You still fall under residential no matter what loan "product" you choose.
2. Yes! If you have even one renter you should have it in an LLC, land trust or both depending on your needs. Refer to an asset protection attorney for more on this.
3. Too many variables here to give you a straight answer. Basically some of the differences between FHA and conventional financing: FHA has a 1.75% upfront funding fee, monthly mortgage insurance which is now 1.35% of the loan, and can lend up to 85% cash out with no hits to pricing (read rate).
Conventional will have hits to rate, (read higher rate), no mortgage insurance and funding fee, but possibly points if you want to get the rate lower. Difficult to give you an exact $ figure unless I have all the details including FICO scores DTI and income.
Really depends on what your long-term plans are for the property. There is no "right" answer unless you have a definite plan. Then you can compare the numbers and you'll have your answer.
One thing to note on the appraisal... lenders wont be using the income method to value the property... it's still considered residential. So your value will be determined by comparable sales in the surrounding area - not your rents.
Hope that helps.