We ended up putting a clause in the lease that we covered utilities (solid waste, gas, electricity, water, etc), but if any single bill exceeded $200 it would be charged as additional rent that was due with the next months rent.

I would rescind my offer and request some additional terms to the contract. 

Does anyway know of a contract that in can present to my contractor that will prevent me from being liable for permit violations?

I would be informing him that he owes an additional $250 above his $1600 deposit to cover the repairs.

Joe has a tax lien for 90K which is preventing him from getting a traditional loan/financing.The house Joe lives in is paid off, but the seller has a lien on the house from his mother's nursing home.  

Additionally, there are some good websites where you can pay for credit checks and/or criminal background checks.

Have you tried to obtain an unsecured line of credit with your new business in addition to your loan? 

Make sure the option is NOT assignable or assumable to prevent above mentioned scenario.

You can request additional security deposit but new laws affect how long you can keep that, I believe only one year but you will need to independently verify this.

Additionally, I reside in the Doylestown area, and would not be opposed to forming relationships with other investors in the tri-state market.