So I would replace plumbing and electrical while I have the walls open if I plan to hold long term (which is what I do).

You will need a primer, and 2 top coats at $1 per sf (each coating) of wall (No thank you!) 

I am not overly-handy (I never owned tools until I bought a duplex) - so far I've done basic electric (installing an outlet, adding a junction box, putting in receptacles, removing breakers, fixing a 3 way switch -- all things an electrician wouldn't touch -- or would charge a couple hundred bucks to do, cost me about 7 dollars - literally), replaced an exterior door, removed rotten siding and put up new siding along with replacing the plywood behind it, re-built the rotten framing of a garage wall, installed a ceiling fan, and just about a thousand other things along the way.

It doesn't always work out that way.... for example, I'm a really good landlord (as I've found out just this year) but the thought of being a landlord makes me want to run straight into a concrete wall.

They have:- kept a ferret without a deposit or approval- just put a hole in the wall- painted all the bedrooms ridiculous colors- Havent oaid their trash bill in over 3 years- replaced all the ceiling fans and did the electrical themselves (without a license)And multiple other things.

Sorry for the wall of text!

I have been told that this can very difficult and costly to do due to opening walls/ceilings.(2) Install a mini split system (outside condenser and wall units) for the second and third floor.  

I am assuming the worst- that the property would need a complete rehab, walls, floors, plumbing, hvac, etc. 1) What are my financing options?

I'm willing to bet that your flooring contractor is charging per sq. foot which means he makes more money by doing it the easy way.I'll be doing a flooring job soon and the only place I will be putting the flooring underneath anything is in the bathroom where it will go under the toilet and vanity only because it would be virtually impossible to install the vinyl planks in the small spaces between them and the walls and the tub. 

Hvac etc Repair walls damagesFix and paint ceilingsPaint wallsNew or upgrade flooring Look at and “fix” curb appealDecide to rent or flipThat’s my basic 10 .