Is there any precedent for a nonprofit ministry founder taking donated funds and buying property in their own personal name -- (not in the name of the charity) and then leasing it to the charity for a 99-year lease? And is this allowed by the IRS rules for 501(c)(3)?
I suspect that there are a lot of precedents for such activity, but that does not mean that it is legal or appropriate.
If the founder just took the money in his or her own name and did not treat it as compensation at the time, it would be an automatic excess benefit in which the IRS would have an interest. (See Ready Reference Page: “Charities Must Avoid Excess Benefits.”) It also sounds like theft and a possible criminal act that would be of interest to the state Attorney General or local prosecutor.
If the founder got the gifts directly from members of the congregation, the members would not be able to deduct the gifts, and there is a serious question of how to characterize the funds in the hands of the founder. It still might be considered compensation to the founder on which tax would be due.
No matter how the founder treats the receipt of the funds for tax purposes, there is still an excess benefit tax question with respect to the terms of the lease and the rent. It must not be more than fair market value.