Yes they have the funds. But don't look for them to make a move to do so. 

They have all their marbles tied up in the Mach E, Bronco, and Maverick. They won't be looking to spend any cash until those vehicles prove themselves on the street without expensive recalls.

American automakers don't innovate. They'd rather pay someone for junk like the MT-82 than spend any time and money on R&D. Just how it goes.

They don’t need to develop one of their own; they can just go back to a Tremec transmission (e.g. TR-6060 or TR-3160).  The MY2016+ Shelby GT350 and Camaro currently use the TR-3160 which is far better than the Getrag MT82.

They could,  but will not.  They are to cheap, and all about the profit.  They could even go back to their old transmission if they wanted to.

Not enough people want a manual

Unfortunately manuals are quickly becoming an extinct species.  

Ford doesn't care about its customers. Profit is all they care about it. There is little point for them to "develop" or even borrow a good transmission for the Mustang.