-I've had a phone meeting with my current property manager who has advised me on local trends and things to steer clear of and will also provide rental comps to compliment the BP estimator.  

Many people are referring to a portfolio loan or asset loan and I am unsure how one secures the refinance loan after going under contract and before the rehab is complete.4) I am having a difficult time estimating rehab costs.

I would estimate that overall wear is probably less than a long term rental, but it depends on who is managing the property.

I would get estimates from both lenders and brokers to see what loan products meet you needs.

Rehab Costs: We estimated the rehab costs to come out at $25000 including labor and materials but we ended up putting in close to $34,500 for everything. 2.

We estimated the rehab costs to come out at $25000 including labor and materials but we ended up putting in close to $34,500 for everything. 2.

This metric is used to estimate the investor's potential return on his or her investment.

Any suggestions on how to estimate rent cost for those rental bedrooms and how to go about creating a lease agreement with the person who is renting?

Flipping requires management of money, people (contractors, subcontractors, realtors, inspectors, lawyers,.....) estimating renovation costs, days on market,..... 

Offering money for an estimate where you are paying for their time or working as much to work with their schedule helps.