He purchased a property in a D class neighborhood and put in A- class upgrades like granite countertops and stainless steel appliance.

The resealing of granite countertops is not something I would put on a tenant, and I am not sure it is a reasonable security deposit deduction unless the countertop is damaged. 

The house will have all new VLP floors, new exterior/interior paint, refinished cabinets, countertops and appliances, new HVAC and roof, fixed siding.This is my hometown.

You shouldn’t.You may want to do tile countertops because they are cheapest, but what if granite is on sale and it only costs 12% more to do tile?

Each unit is 1800 sq ft with high end features, such as: Granite counter tops, top of the line cabinets and vanities, 10 ft ceilings with crown molding, top of the line appliances, wide open floor plans with travertine floors, 3 beds 2.5 baths with a garage and an upstairs balcony.

Does anyone have a go-to “guy” or company that sells remnant countertops for cheap?

It depends on your local fashions, of course, but you don't see too many wooden counter tops these days. 

The place is really in perfectly adequate condition, but our plan is to go in and take it to the next level... replacing carpets with wood plank tiles, installing glass tile backsplash , staining kitchen cabinets dark and adding satin nickel pulls, adding stainless appliances, a dishwasher, disposal, built in microwave, resurfacing countertops...

Do they have the same quality of counter-tops, kitchen appliances, flooring, bathrooms?

Counter top quality (Granite verses laminate) will make a difference in appraisals.