I bought a couple Samsung Micro SD cards (64GB)..

They sure look real, packaging and all. Turns out, they are bootleg and testing states they are 8gb cards. Research tells me that I am not the first, and this is big business.

Is there anyway to reprogram the memory card controller to the proper size?

They would at least be usable.

I am a hobbyist, not a pro. I have serial ttl equipment as well as jtag.

I know form a cost standpoint it is not worth the effort but it might be a learning experience.

It will be quite challenging. You wouldn't use TTL or JTAG, but the software referred to as MP Tools (Mass Production Tools). You might find the tool for your specific card at somewhere like http://flashboot.ru/ or http://www.usbdev.ru/.
Problem is, it is critical to identify the controller in the card, and this is likely been obfuscated to look like something else. Then you need to know the memory chip as well so you can program the controller firmware. There is little documentation, and even if you were to succeed in programming it, I would never trust it for data.

there are a couple of tutorials online for reprogramming fake flash drives, but be careful - there are also quite a few website that host malware and also trojaned flash drive tools around. Common indicators are large blocks of text with a fake clear image over the top, so that clicking to select text or on buttons will result in a redirect, or malware install.

Thanks for the advice..

I probably won't go any further even if I get lucky and succeed. As you said, it could not be trusted.