Then hopefully you can still add in a profit.

Then when we sell, get back my renovation cost and split the profit with the seller.This would cut down on my cost of money and turn a reluctant seller into an enthusiastic JV partner.Good idea?

If there's a profit in the end my taxable income will be reduced thus offsetting the tax I paid in earlier years, so, I think it does 'zero' out.I don't think anybody truly understands how this all should be done, probably not even the IRS. 

I made some profits.

What I am looking to accomplish with you guys is to build lifelong profitable partnerships through single family/Multi-family wholesale and flip projects.

Is the potential profit better since the loan is less with borrowing on a lower purchase + rehab?

Without seeing the property, all of those fixes you listed could easily cost the difference between the purchase price and ARV, eating up your profit- make sure you are comfortable with your numbers. 

I want to get the lot under contract and then sell the contract so I need to be sure I can make a good profit on this.

My uncle and I have talked to the president of the non-profit and they are interested in selling it, and would take what is currently left on the mortgage for the sale since they would disband the non-profit.

Unless those expenses were paying him and other family members to reduce his " profit" keeping within the bounds set by HUD .Who says my brother in law isnt worth $125,000 a year to change light bulbs .