The tile flooring did not match throughout the house, the grout lines were not even, and some areas around the edge of the time had almost 2" of grout instead of cutting a piece of tile for the edge.

I did completely renovate the rest of the units, kitchen, baths, floors, etc so I don't expect to have major expenses aside from the ones I mentioned.  

We are putting in new floors, total paint job inside and out, new kitchen.

They can't handle the paint and floors though.

The seller told us, the house needs EVERYTHING, from roof, kitchen, bathroom, floor, wall, ceiling, lights, lawn, doors, it's pretty much a big rehab.

Ok BP family finally got my first house that I will be house hacking in a few (hopefully) but I'm having a issue with the first floor tenant.

(HVAC and water heater are end of life, plus needs interior/exterior paint, flooring, and other significant but not major issues). 

I'd personally be doing the framing, floors, sheetrock, HVAC, among other things.

It would be a good ideal to paint all treated areas with a stain blocking primer including the wood members, studs and sub-flooring if affected.

Also keep in mind that if the basement is below grade it won't meet minimum standards of fitness for human habitation:"No room or area in a dwelling may be used for habitation if more than 1⁄2 of its floor-to-ceiling height is below the average grade of the adjoining ground and is subject to chronic dampness."