- Is all of the equity from your land sale being transferred (through a Qualified Intermediary) to only the investment/rental portion of the new property? 

We transferred the title of the property to an LLC where both myself and spouse are 50/50 partners.

Is there a way for the property owners to get those accounts transferred, or are they stuck with that real estate agent forever? 

Those funds you can use as you wish, the loan has to be paid back within 5 years using amortized schedule.Properties you purchase in your 401k belongs to the 401k and you can't transfer, sell or convey them to you or any other disqualified person.

I was expecting these reservations to be transferred over to me upon closing.

I know a lot of people who do it, I would ask what is your exit. for example we have done it when we were doing some renovations and had a line of credit as well that we were going to transfer the cost too.

@Kyle Steiner more than likely they will have you do an interspousal transfer.

@Denise Evans If the heirs have not taken action to move the title into an estate, or to transfer to an heir, how is the state supposed to know the person is deceased? 

I would rethink actually transferring the deed to a buyer if you are still on the hook for the note.

If you plan on transferring the property into an LLC (which I agree with @Jonathan Klemm, is not always necessary or recommended) then you will have to register is with Indiana at inbiz.com if you did not form it in Indiana.