Is there another way to find out which local banks do commercial loans that meets this criteria?

If your using financing the bank requires this.

And 2) I have heard there are challenges to refinancing with a bank under an LLC?

Much like "ratholing" in poker where the player takes his chips off the table and ends up only playing with the banks money. 

Typically you will want to work with a direct to FNMA lender that doesn't have any overlays, but smaller community banks or credit unions that service their own loans could work as well. 

That makes it a MFR and the bank wants 25% down.

I have 50k in my bank.I haven't check lately, but last time I check Banks don't want to lend self employed any money to buy rental properties.Is there a way to re loan on my rental property so I can use that to buy rental?

The first you should realize, If you have not figured out, that there are other lenders that will require less down payment other than a Bank. 

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We are using bank financing so each member is responsible to pay the down payment plus closing costs equivalent to their percentage of interest in the company.As far as the payroll taxes or 1099 that is something our CPA will be guiding us through.