A contractor took out the carpet and disinfected the contaminated areas and installed 6 fans to dry out the walls for three days. this costed $1900The next part is to install new carpet and install baseboard trims in the areas previously removed. they quoted me $3500 for that work.So total damage is around $5900Since this is my first time rental I need your advice on what to do.Should I directly bill the tenant that amount and ask them to pay it immediately?

We do the windows, get rid of dust and cobwebs, do touch-up, cut down/trim any bushes, etc. 

New roof, new flooring throughout, removed popcorn ceilings, 2 new bathrooms, new kitchen, replumbed, new lighting, all new doors and trim and a ton of paint.

I was trying to research online and it was mentioned that the neighbor that has incurred damage could have hired an arborist when he noticed a problem and have the roots trimmed before it led to more damage. 

You can see it in the pictures of our Buy and Hold Rental featured on my profile, it really makes the white trim pop and look fresh.

Using a vinyl product that is watertight in the field, I intend to first lay a thick bead of polyurethane exterior-grade caulk (Vulkem brand for instance) at the wall perimeter against the sub-floor and bottom plate and under the wood base-trim, and also at the door threshold, keeping water inside the bathroom.

Now, I UPGRADE my duplexes not with swimming pools mind you, but with microwaves over the stove, granite countertops, replace small and out-dated baseboards, replace carpet with luxury vinyl floors, upgrade to LED light fixtures, up-date faucets, new-used appliances, six panel interior doors and contrast paint (white ceiling, Light beige or grey walls and all trim white).  

-stone, masonry, framing, drywall, nails, sheathing, cladding, roofing-wall & floor tile-windows-doors-fixtures-finishes (counters, cabinets, trim, paint, etc.)So far, it feels like we're paying retail for everything, apart from the 5% discount at Lowes etc.

I can’t really trim my investor count down to the lender desired < 4, and I’m not sure getting the investors to form a separate LLC just to pool the capital is going to fly either. 

Meanwhile, I already have a set of contractors (framers, plumber, electrician, HVAC, drywall, etc) so I'm ready to be my own GC and also DIY some of the finishes (trim, tiling, painting, etc).Does anyone know if there is a way around this?