I think the sale triggers a change from passive to active and it can be used to either lower basis or offset capital gains/depreciation recapture and if any is left your ordinary income.  

Nope says the driver with a lock and chain in is hand.

The fha 100 mile rule will be triggered whenever you try to vacate your current primary and also trying to use the rental income to qualify.However, this 100 mile rule can be exempted for the following rulesRelocationIncrease in family sizeVacating a joint owned propertyNon-occupying co-borrowerIf you are not trying to use FHA on your 2nd househack, you can use conventional and the rules that I mentioned above will not be a concern.

If I were you I would reach out to the mortgage holder to get permission to transfer the property to the LLC without triggering the clause.

Most investors are doing LLCs from my experience... but that doesnt mean you have to. there are some liability protections with LLC, along with a little anonymity if set up right. but also some added costs. one suggestion here is just whatever you decide, stick to it. some counties will see a transfer between personal/ LLC or vice a versa as a 'sale' and trigger property tax reassessment.  

On the other hand, I am locked in at a 3% interest rate on a home that will likely continue to appreciate well.

I’ve been doing my due diligence for over a year now and I’ve finally come to the point where I need to pull the trigger.

Sometimes listing agents will be opposed to taking an offer with a VA loan because they can have a more strict appraisal but it's still very achievable to lock something up with one. 

C) Or, do you just keep the door, still keep it as one unit, but basically separate your renters' and your space with a lock?

As you get contracts locked up, feel free to reach out as I can help you with funds for EMD or Double Closing, if necessary.