Bust a pipe in a dark crawlspace and you will probably find mold growing there if it sits for any length of time.The good news is there are some things you can do yourself if the problem is not widespread.Dry it out, turn on the lights and circulate air will kill most of it.

You don’t want to close on the house and then go and find out a tree fell through the roof last week or a water pipe burst.

After being under contract for the property, a pipe broke and flooded part of the downstairs unit, I was never told about this until after closing (by tenants).

Old houses come with cast iron outflow pipes.

Is it clay pipe, cast iron, or some type of plastic? 

I'm concerned that it might be tree roots growing into the pipe.

If you exhaust all options and no one will finance you, I'd say save up all the money you can and hit it hard when you graduate.Best of luck to you :)

A 4,000 sf house is a big house, but $30 to 40k to re-plumb a house that only has 3.5 baths with new hot/cold water piping sounds extremely high. 

They have squatters, or all the piping and wiring has been pulled out, or the listing is fraudulent.

Sounds honest, too.  10% for mom and pop owners with less than 100 units is a pipe dream.