However, strange things happen, her x boyfriend may have had ID, put her down as a co-tenant, the landlord didn't meet her, he bailed, she could have been named and she'd never know it!

If you want 4 in your name try using him as a co-signor? 

She is holing 51 percent of the company for credit purposes on paper, but will maintain as a silent partner.Our initial idea was to Refi her primary residence to capture the existing 140k of equity in the home and to take that over to our new LLC as starting capital.We have hit a months long snag with the bank who is requiring a co signer as the only way to move forward.

I am also looking to have my roommate be a co-borrower, but not a co-signer.

If you put him on the lease as a co-applicant, he will have equal rights as her. 

Would a co-signer typically be enough for the second mortgage?

I have a non-recourse term sheet from a lender that is requiring me to get a co-sponsor to meet the net worth requirement. 

My question is, if I bring a co borrower in to show proof of funds will I still be able to get that 3.5% down? 

Then if you end up needing to purchase that property for cash you can always add those outside proceeds to the 1031 proceeds at that time.You're absolutely right about lenders not lending without a CO. 

Anyway, I ask because I had a conversation with a co-worker that I would always try to work with someone that hit on tough times if I could, and a crazy idea like this might really put a smile on my tenants faces and better yet, provide even more loyalty to produce less tenant turnover.