Is there a workaround, like a "thunking layer",

No. You cannot call 32-bit dlls from 64-bit code.

Or is there a module like Win32::API but for 64 bits

Not that I've found, but there could be.

The biggest problem is setting up the stack frames for the 64-bit calling convention without using a compiler.

In many ways, the 64-bit calling convention is much simpler than the (various) 32-bit calling conventions. For a start, there is only one of them, and all parameter types are passed as 64-bit entities, mostly in registers.

However, the removal of the _asm{} functionality from the 64-bit MSVC compiler means that you'd need a spot of MASM to facilitate the interfacing. Trouble is, the 64-bit MASM is extremely limited.

It might actually be easier done with gcc with its built in assembler facilities, but that assembler is just weird.