If you think making house payments is not investing, try renting.The trouble with relying on statistical metrics to make blanket conclusions is that it's silly and those metrics never reflect reality anyway.

I've had some time now to reflect on this experience and assess why exactly I was frustrated.

As always, it should be taken with a grain of salt (unless it's an actual result and reflected on the rent roll) but they're usually able to provide a good high-level number.

As far as the rental income in the subject property being counted as income for the borrower, the FHA manual states that for borrowers with limited or no history of rental income from the subject property, the lesser of 1) NOI reported on Freddie Mac form 998or 2) 75 percent of either fair market rent reported by the appraiser, or the rent reflected in the lease agreement(s). 

Clearly I need to update my lease to reflect that moving forward! 

Do I just wing it and go with a generalized assumption like a best case/probable/worst case scenario and get my lender/partner to say if rehab costs are estimated to be in the best case/probable scenario then were clear to go other wise the MAO would need to be lowered to reflect the increase in rehab?

I’ll edit my profile to reflect the value I would like to glean from a mentor or partner.

Your budget does not reflect that, did I miss it?  

Also how should this be reflected on the lease to avoid putting down lease start date of 15th and do 1st instead ?

Those costs should absolutely be reflected as R&M.