After Feb 28th, you could qualify for cashout under Fannie/Freddie.
It does not matter if the original loan was Fannie/Freddie. You can refi under whatever program you now qualify for.
The issue with financing as a primary residence is not what you might be doing later. The issue at time of application is what is your "intent" at that time. You will have to satisfy the lender that you "intend" to move from your current residence and make one of the newly financed units your primary residence. Whether you have someone basically house-sitting your unit while you are away is not paramount.
You must keep in mind that since you are dealing with a private, portfolio lender, they can do almost whatever they want - under the law of course. They are not operating under Fannie/Freddie/FHA rules, so a third person (like myself) would be hard pressed to say/know what they will do
These credit scores will not get you a great rate. We must go by the lowest mid score of both borrowers. So, the score that would determine your rate is 650. Your wife's score would be meaningless.
No, you could NOT get your own appraisal. Never, ever. As the lender, we MUST order the appraisal from a licensed appraiser accepted by the lender. Having a buyer get their own appraisal would open up wide scale fraud. Or I should say, "more wide scale fraud."
There are a few items on your tax return that could call for income recalculations IF not revealed at time of application: lower allowed self-employment income, lower allowed rental income, unreimbursed employee business expenses, alimony, dividend and interest income, wide variations in commission/bonus income from prior years.
You have a nonstandard transaction that a nonportfolio lender would carefully scrutinize. You haven't said how much equity you have. Unless you have a LOT of it, some lenders will deny your loan as an investment/cashout at a score of 650. Shopping around for bare bones rates might get you nowhere except for a drop in your score as more and more lenders pull credit. For mortgage pricing, credit scores are tiered and you could easily find yourself facing a higher rate if the score drops by a mere 10 points.
If I were you, I would instead find a good deal and take it
Every borrower wants the lowest rate Josh, but you have to be in the drivers seat in order to find low pricing.
You also haven't stated what the loan amount would be. That could change things too if it's jumbo. And you didn't say how many units. All these details affect rate.
Again, for a portfolio lender, no third party can tell you what they are going to do. They are lending THEIR money and they make the rules.
I would suggest you contact a Fannie/Freddie lender and get a quote. Then compare. Your situation is not the norm and you owe yourself a consultation with a professional. There are far too many ifs/ands/buts for you to get all the "right" answers here.
You can try putting in a request for a rate quote at www.zillow.com. Be sure to provide them ALL the details of your transaction. Bad input, bad output.