I am not at all familiar with the details of the NSX R final drive. If your primary concern is the error in the speed signal for the EPS caused by the change in the final drive ratio I personally would not be overly concerned. The change in drive ratio will mean that the pulse / mph is higher than with the standard final drive so the EPS receives a speed signal that is higher than true speed (the % error being the difference between the drive ratios). This should cause the EPS assist to taper off faster than normal which some people might view as a desirable feature.
Just for good measure, the 97+ EPS unit has two speed signals. VSS1 comes off the same VSS sensor as is used for the speedometer and ECU. VSS2 comes from the pulse unit from the differential mounted sensor. For double good measure, the VSS pulse rates for the two signals as measured at the terminals to the EPS control unit are different. According to the service manual VSS2 is 50 pulses per revolution and VSS1 is 4 pulses per revolution (presumably revolution refers to a revolution of the rear wheels). The service manual is not clear on what the EPS does with the two signals other than generating an error code if there is a discrepancy in the derived speed signal between the two. Perhaps it defaults to a minimum assist level?
I know physically where the VSS1 and VSS2 sensors are located - pretty much side by side on top of the differential housing. VSS1 is a mechanically driven hall / opto sensor (I am guessing that the drive is right off the final drive gear) and VSS2 appears to be a 'tooth counting' variable reluctance sensor (it only has two wires) presumably sensing the teeth on the final drive gear (or is there a separate tone ring?). Presuming that both VSS devices get their signal off of the final drive gear the speed error caused by the change in final drive ratio will be consistent and should not cause any error codes for the EPS. In such case the only change is that the assist may taper off faster.
If the problem is that the VSS2 sensor no longer works with the NSX-R final drive because of an absence of a tone ring (or whatever reason), that is a bigger problem. In such case, if you really want an NSX R final drive I would be inclined to try to fake the VSS2 signal by picking up the VSS1 signal and writing some pulse multiplier code for an Arduino that could then generate the higher frequency VSS2 signal. This will work just fine for steady state speeds. While changing speeds there will be a short time lag between the calculated VSS2 signal and VSS1 which creates a potential speed error between the two which might trigger an error code depending on the EPC speed error threshold. A GPS receiver with separate controller could generate the VSS2 signal and presumably do it fast enough to avoid generating speed mismatch error codes in the EPS.
However, GPS units are not without issues. I have a GPS speedometer on another car and I know that there are certain times of the day that signal acquisition can take minutes, presumably because of the available constellation of satellites. Once acquired, I have never lost the signal as long as I stay out of well shielded structures and tunnels. One additional problem is that the GPS based system is not affected by tire size. If you change your rear tire size this cause an error in the VSS1 signal while the VSS2 signal remains true which then creates the potential for a EPS error code. The faked VSS2 signal from the VSS1 sensor would not suffer from this tire size change error.
Not being familiar with NSX R stuff, the higher ratio final drive creates a potential problems for the speedometer on the R. Does the NSX R use a different VSS1 sensor to give a correct pulse rate or does it use a speedometer that has a different calibration to work with the different pulse rate associated with the NSX R final drive?