I also don't recommend you stretch yourself so thin.

If there is rot and its a more extensive of a job than merely replacing the window that will drive cost as well so you should seek a line item budget from the installers.  

In the near future id like to move out and purchase another similar property but I'm trying to maximize my income and property performance before hand to give myself the best chance at qualifying for a fha loan 3.5% down.

I learned that there is a company in Austin TX named Homemade that performs this service but there is no information on what they charge and what their ageement looks like.

This is a company that will perform scheduled inspections of your rental property to identify deferred maintenance needs, dubious tenant activities (say, illegal pets, bad housekeeping, failure to change HVAC filters etc). 

I always steer clear of Angie's List, Yelp, BP Vendor, Dave Ramsey Select Vendors, or any other service that charges the vendor for membership and then promotes the list to the public as if trust, excellence, and performance have ANYTHING to do with the list selection. 

Deposits are made as they come in and they don't jack up the price if the loan becomes non performing.

I have home equity that I could use to get going, however it would be a stretch to handle both the acquisition and repairs of a property.   

You will want to perform a proper dry out of all materials and replace as needed, treat the area and have the lid put back together of the downstairs unit.

Not to mention, they are not legally able to perform any of the duties or services they accept payments for.