Turned out that a few joists had some pretty major scarring, I had to "sister" onto them, everything else was "cosmetic" although the smoke penetration into the sheetrock and slab needed some heavy duty sealing to eliminate all the odor.The second one was a fire that the seller wanted about the price of the land it was sitting on.

Now that the floor is very clean, the enzymes should penetrate the floor with ease.

Im currently dealing with this now so this came from the plumber He is trying to fix a drain, not hot and cold supplies, there should be no supply connections to his drains.But the trenchless solution will only work between two points with no branch arms, if branches exist, they need to be hollowed out later and it's really tricky.Also, trenchless epoxy liner is not a good match for a tree root penetration issue, because for that to work optimumly you need to have the interior of the pipe rimmed round and jetted clean prior to applying the liner, or else the liner will assume the shape of whatever debris is inside the pipe, if it's a chunk of tree root, then your liner will take the shape of that tree root.

Without sealing the air penetrations from conditioned to unconditioned space, the insulation R value will be strongly diminished and the dust, draftiness, high utility bills, etc will continue. 

In order to remediate mold, you need to remove the affected areas as well as locate/repair the source of the moisture.

I saw wet ceiling in basements that seems to be a plumbing problem but turned out to be a roof problem where water penetrated the space within the wall and travel all the way down to the basement...

We've learned to inspect at least once a year or so and fix all the tiny things before they become major deals (painting outside door trims before moisture damage sets in, trees growing through decks, fence pickets loosening, etc.).

Replace 1 to 2 Windows (moisture issues): $600 Miscellaneous Other Cosmetic Issues - up to $2,000.

You will also need account for fire-separation [5/8" sheetrock; penetration/through-wall collars on plumbing/electrical, etc] between the garage and the loft unit.

That would get the air circulating and dry out any moisture.