The simple things are roof, windows, siding/exterior, exterior doors, mechanicals, plumbing risers/laterals.

No plumbing, electrical, windows, fixtures or mechanicals.

I feel like I have the theory and the mechanics down for house flipping thing.

It's nearly impossible to see every difficulty that may present itself... anything from Mechanical failures, Roof problems, Electrical or Plumbing problems, Structural issues, etc.Most importantly... know your end game.

We had to fire a contractor, who then put a mechanics lien against the property.   

It is possible that a contractor will put a mechanics lien on the property prior to closing.

Same scenario as above except that the principal on the first is $125k.I have a feeling that the answer to the next question can be inferred from the answer to the above question, but what happens if I own the second (say I bought a mechanics lien/judgement from someone) and the first is $50k and the lien I bought is worth $10k and the property is worth $150k.  

Doesn't seem like your analysis has any account of all the repairs needed to make rent ready.Sheetrock:  $25 to hang a sheet, $25 to skim/patch a sheet, plus the cost of each sheet.Paint: about $250 a room depending on how expensive you go with paint.Flooring: $2 - $8 a sqft depending what you end up doing Get all the mechanicals checked out as well.  

Roofs maintain the integrity of the rest of the house and should be maintained as such.The price in which you purchase the property should factor in the age of the major mechanics along with windows, roofs, and siding considering where they recommend in their life cycle. 

Guess what, if I don't like what my mechanic charges me, if I think the fee is completely outrageous, I don't call him an unethical crook, I find a new mechanic.