It looks like the N64 uses 3.3V for communication. Why not write all the stuff the MCU does in C and control the whole thing via parallel port? (
http://en.wikipedia.org/wiki/Parallel_port#Pinouts)
There are 8 to 11 output pins, which can be used for data, and 4 to 7 input pins, which can be used for polling. Is that enough for this design?
Two problems: timing and availability of a computer with parallel port.
The timing is a programming issue because I think, that every modern computer is fast enough to handle N64 polls.
As far as availability goes, there are USB to parallel adapters, ranging at about 3,50€ or 4,80 $. All you have to do is put a socket on the parallel port side of the cable and use a ribbon cable to connect to whatever hardware you want to connect to, e.g. a N64 controller. That would take another 3 to 4 $.
If this works, you only need the USB to parallel cable (or an older computer with parallel port), the parallel to N64 adapter and the software. Furthermore you'd be independent of the filesize of the m64 file. File converting, if required, can also be done in C quite easily.
Of course it depends on the design, whether this could work or not, but it'd be an absolutely low cost and highly portable solution.