If you added a pet addendum, then it sounds like the pet is no longer an issue, or grounds for any legal action.That leaves you with the unauthorized occupant, However, if you have been accepting rent payments despite knowing about the unauthorized occupant, you've essentially given them permission based on the legal principle of waiver.

You will sign paperwork saying you are going to live there and failure to do so is a crime. 

I have a partner that is willing to co-sign because he has proper paperwork including these pay stubs.

(yes we were paying $2800 /mon for PITI+HoA as it was originally our starter home, but I figured $2400 is essentially sunk cost because that was market rate for apartment rentals in the city.

The issue is I only ever spend 1 week/month at most in Milwaukee, so I’d essentially need to buy these properties sight-unseen.

Less paperwork, no up-front PMI, and monthly PMI goes away once you hit 78-80% LTV.

I'm also a Realtor and was essentially my income was impacted 2-fold.My question would be if I accept the loan, should/could I simply open a separate bank account and pay myself and/or other employees a wage/salary.I was going to give myself a wage this year, but since I didn't have any deals, prior to the lockdown, I didn't apply any (therefore also lost out on PPP).

This seems to be referring to what is often called a "Registered Agent", or someone official in the state who should always be serve-able in the event a process, notice, order, or other legal item needs to be served.For example, many states require every LLC to have a registered agent, which is commonly the attorney that filed the company's formation paperwork. 

They do NOT get involved with deal paperwork besides using it as a guide on what to do if mutually accepted.

There are a few other negatives about FHA that you're not considering:Lots of extra paperwork with a FHA loan.Contractors must be approved by HUD to do the work, so that limits who you can hire.