A) Net operating income is the money you have to work with after you pay your reoccurring bills. So if you get 1500 in rent and your PITI are 1000. your NOI for that month is 500 which you could decide to set aside for vacancy, repairs, cashflow etc...
B) Dont get too caught up in the 1% or 2% rule, its just a rule of thumb. I would use it on your purchase price plus repair costs. Focus more on the cashflow and ROI.
C) Purchase price is not necessarily market value. Purchase price would be what you actually got the property for. Market value is what the house is worth based on comps in the area. You could purchase a property for well under market value if you are a good negotiator, if the seller is motivated to sell and you can close quickly, or if the property needs significant rehab.
Net operating income does not really include holding costs while rehabbing because NOI is a factor when the rehab is done and the property is rented out. There is no NOI if there is no rental income yet.