My intention is to replace the manager with a paying tenant and manage the property myself.

Clarify his intent and proceed accordingly.

If you're looking for something passive so that you can focus on your job and other obligations, buy & hold rental property could be the best route to take.If your intention is to run a marketing campaign to find deals and sell them to an end user or other investor, wholesaling could be your best bet.No matter what you choose, please find someone in your market with market knowledge and experience and offer them coffee, lunch, or volunteer your time to add value to them somehow. 

The 90 day timeline came from the 90 days of intention journal I just picked up.

A contribution of property to a multi-member LLC could effect the ownership percentage of the LLC in ways you do not intent to. 

My  intent is to keep them long term.  

When things have escalated on his end in the past I have offered him the option to break his lease and he has made it very clear that he has no intention of ever leaving (just complaining forever, lucky me).

My intent was to purchase another rental.

Explain to them your situation and show that they mislead you (intentionally or not doesnt matter). 

Also, he called my GC about the intent of the property and claims that supposedly another resident called and complained that they weren’t allowed to make their house a duplex and rent a portion so why am I?