This is a pretty involved flip for a first timer and I'm crossing my fingers for you. I can't imagine doing a 3/1 for a flip but I don't know your market and, these days, I don't take anything I do to full retail. We buy ,repair, rent & sell to passive investors looking for at least a 10% net return.
On the mold, you will see varying opinions from a lot of well meaning people. Mold is serious stuff. Before you start work in the basement, I'd suggest you turn off the hvac & mask any vents to the basement area. Get some Microban and thoroughly spray down everything..and I mean EVERYTHING before you start removing anything. Once you get the drywall and paneling out, spray everything again. Microban is the industry standard and kills mold on contact. The problem with blogging is now you've publicly acknowledged the presence of mold in the property so handle it properly. A pair of $12.hr workers isn't going to handle it properly and, if there is a problem with it later on, you might be on the hook for far more than you bargained for. Mold is very serious stuff and can make you sick or even kill you if you mess with the wrong one. Always wear a respirator when working with mold.
Is there a way to add a 2nd bath to the master.....somehow splitting the existing one? What would that add to the resale in the area?
I'm not sure why you want aluminum fascia and soffits...except to cover up the rotted wood....which you really need to repair the wood FIRST then cover it over if you wish. I'd just repair, prime & paint everything. I prefer seamless 6" gutters with 3"x4" downspouts on most of what we do. We fabricate them onsite and hang with hidden hanger screws. We usually do this as it's best for long term maintenance.
I'm not sure if the flooring budget includes the new tile for the kitchen....or is that in the kitchen budget? If it is...then you're budget is low. We use screwed down underlayment on our tiled floors...be sure they don't use roofing nails as that's a standard practice. We are working on a home right now where the kitchen tile is all cracked and bucking because they nailed the underlayment. The cabinets look great for a retail flip.
Take a look at your market and run through some of the houses in the $200k+ range and try to duplicate some of those finishes in your homes. Even on our flips, we use nickel or bronze finishes and always spend more on ceiling fans.
Happy Investing!!