The fact that you have a small amount of charitable contribution income should not prevent you from being a public charity if it is from a sufficient number of qualified sources.  Expenditures have nothing to do with your public support status.  A major bequest would normally be considered an “unusual grant” and would not count in the public support calculation at all, although significant investment income that goes only in the denominator of the fraction could flip you to private foundation status in future years.   (See Ready Reference Page: “Calculating Public Support”)  Therefore, you probably want to get the endowment out of the smaller operating entity.

If you are still a public charity, giving money to a donor advised fund would convert the distribution from the DAF back to the operating entity into income that would qualify as public support (under current rules that are under review by the IRS) and would help your public support qualification.  Unfortunately, if you give the funds to a DAF sponsor, you lose control over it. But since it is an endowment from which only income is available for current expenditure,  that may not be the end of the world. 

If you are now a private foundation, a DAF sponsor would have to exercise expenditure responsibility on distributions to a private foundation, but you may avoid that requirement by making it a fund designated only for your use, and not a donor advised fund.  If you hold the funds in your present organization as a private foundation but can’t spend the income effectively on a current basis, you could make the balance of the 5% payout requirement to a designated fund at a community foundation to be held for expenditure later.  (This rule that currently permits this is also under current review by the IRS.)

If you are still a public charity, you might create a “supporting organization” to hold the money and provide the cash for the acquisitions you anticipate later.  A supporting organization has no annual distribution requirement, but it loses its supporting organization status if the supported organization loses its public charity status, so it could be risky in your situation.

You could also consider setting up a controlled 501(c)(4) social welfare entity with similar charitable purposes that would not be under the standard private foundation rules and would not have to meet an annual expenditure requirement.

There are a variety of opportunities that might work alone or in some combination, so you ought to consult with an attorney who understands these issues.  You may need to get the approval of your state Attorney General or a court to move a large amount of endowment from one entity to another, but they are frequently cooperative when the maneuver saves funds for local charitable purposes instead of paying significant excise taxes to the feds.