is there a way to over come this limitation on RAM, like how you said Windows 3.1 only works with 64MB of RAM?
not using RAM wouldn't be the least of the problem if you tried to run Windows 3.1 on a modern computer. Even assuming DOS 6 Fdisk will properly recognize the Hard drive, you still can only make partitions up to 2GB in size (fat32 enabled DOS 7 notwithstanding), which limits you to 23 (letters C through Z) times 2GB, or 66 GB. Even then, it's using a ridiculously large cluster size, leaving a lot of slack space. And good luck finding a Video Driver in windows 3.1 written for a new Geforce or Radeon, ditto goes for most sound cards, and I don't think there are drivers for any Wireless cards either.
And if one was to do so, say good-bye to any "advanced features" of the motherboard, like ACPI or Hyperthreading, or, well, pretty much any extension, like SSE,3dnow, MMX... Heck, Windows 3.1 only supports PCI when drivers expose them as ISA, even then their are problems.
And even with 64MB of ram, GDI and USER heaps (as mentioned previously) are limited to 64K, and their is a limit on the number of "selectors" (memory handles, I believe) that can be allocated. Once those are exhausted, it won't matter if you have 2MB or 2GB or memory, it won't be able to allocate any more (usually followed by a terrific crash, including fonts reverting to system.