Establish a self-directed IRA.

Hello John, This would not be a requirement of the IRA custodian.

I was originally just going to transfer the Roth part into my existing Roth IRA and setup a Traditional IRA for the pretax funds but I'm thinking at the very least I want Checkbook Control on my funds and that's not available with my existing company.

I have a self directed SEP IRA, with about $25k in it.

A good Solo 401k or IRA LLC provider will have a lot of information on these topics. 

Purchase price: $300,000 Cash invested: $42,500 Sale price: $400,000 I purchased a home within my self directed IRA.

Would it be worth it to cash out our Roth IRAs with the exemption clause allowing no penalties for first time home purchase?

I wholesaled it to my broker, then we partnered with private lenders IRA's to fund the deal.

Don't, unless it's the first $500 for real estate after max-funding a Roth IRA invested toward outcome goals.

All of the profits going back to the Self Directed IRA tax free.