According to them the only idea the IRS will be looking for is if gains are exempted that they qualify to be exempted.  

One simple planning devise most do in their estate plans is to combine the estate tax exemption for each spouse in a trust (called an A/B trust).

If we sell the unit now, it is still considered a primary residence (lived there for 2 out of the 5 years preceding sales) which will exempt us from capital gain ($250k for single; $500K for married filing joint).

You're also exempt from cap gains if you've lived there at least 2 out of the past 5 years.

IRS section 121, primary home sale capital gains exemption.....assuming they occupied the home.

The title company is asking me to fill out the 1099-S to report this property sale, but I am not sure which EIN to write on that form: of the employer (plan sponsor) or of the tax exempt plan?

There are some exemptions for not having to add an extra parking space for the ADU.

On a side note, The House Ways and Mean Committee has released text on a bill aimed at exempting certain balances in IRA from RMDs. 

You also still qualify for the 2/5 primary residence exemption. 

You meet the use requirement for the primary residence exemption now.