I am currently looking at a MFU in Philly to be financed via a low money down conventional mortgage. 

The rates are a little higher then conventional but not as high as HML.

I put 5% down using FHA and I am now thinking about refinancing into conventional to get rid of PMI and re-use FHA again in the near future (1-3 years).My question is, if I pay for an appraiser to come out and give me a market value on my property, can I use that number and report with a bank or will the bank want a separate appraisal done?

I don’t know if this helps or not, but the loan is going to be FHA 203k, or Conventional (depending on if the repairs are serious enough or not) Thank you very much!

My gut says that would not fly, but then again, HML don't seem bound to the same standards as conventional. 

Tough to get comps in the area - not much inventory.

(Having been a lender, I know that the bank's decisions are made on things like VA, FHA or conventional, if it was a purchase loan or a refi, homestead, quotas for the negotiators, pressure from the FED, incentives for the negotiators, loan modifications, bankruptcies, lawsuits, robo-signing, MERS, bank's availability of funds, vacant management positions and on and on.

Your daughter will benefit far more in a conventional school setting than she ever will being "home schooled" and you and you wife will be able to work equally and move forward at a much accelerated rate.

The thing i am considering now, is if i want to do a 100% VA cash out refinance to pull about $80k from the home or refinance it as a conventional loan to free up my entitlement to use again to buy another home zero down

There are some 3% down conventional loans with lower PMI rates.