You have three choices...transfer the property and keep the loan in tact hoping they won't trigger due on sale, refinance into a loan that allows it, or simply leave things as they are. 

Yep, then you will probably need to move the cash.  

Fannie/Freddie (Conventional) loans aren't just about rate and transfer taxes. 

If one is transferring property title from personal name, a Grant/Warranty Deed would be drafted/recorded to transfer title. 

With actual cash, you just transfer it. yes, but you can still bid with lender approval - without appraisal contingency - you send in deal (app), it gets approved by lender its functionally the same as cash (except in true lightning speed situations where there is a quick auction with little time to prep but thats generally pretty rare I'd think)Right, but that's not cash or functionally the same as cash because the lender can change the terms at the last minute, as often happens with less experienced hard money lenders.

If there is a renter in place, you may be able to do a cash out loan without changing who owns it. 

If I want to transfer my title to my younger brother, what is the best way to do this?

I am wondering if transferring the cash periodically to a standard brokerage IRA account may be my best option.

Eventually, I’d like to start using the cash flow to pay myself and work toward replacing my day job income.

If you don’t pay the tax when you transfer the stock to them they’re going to owe the taxes on your gain and you haven’t really “paid them back”.