I dont know anything about this Midi interface, but would be interested in helping if I can.. I am in the process of building MIDI into my Theremin at the moment, so it would be interesting..
If you could post the instructions / schematics somewhere that I can access, I would look them over.. you could deposit these at E-14 Theremin Resources (http://www.element-14.com/community/groups/theremin-general-resources) as .pdf or whatever.
Messing about with the MCU frequency is probably not the best idea.. If the MCU has an on-chip UART to generate the MIDI, then keeping the baud rate from this UART at 31.25kb is critical (Maximum deviation allowed is +/-1%, and one does not know how close to this the UART is actually running - another 0.5% could be enough to make MIDI fail) .. Changing the master oscillator / Xtal will (most likely) completely mess up your MIDI.
Also, Messing about with the frequency is most unlikely to solve the problem anyway - The process of deriving pitch data in a MCU is (a lot) more complex than just counting clock pulses - there are many processes and ways it could be done, and depending on the processor / method, you will find different outcomes from fiddling with the MO.
Not knowing anything about this pitch-Midi interface, what follows is pure theoretical guesswork..
Midi Messages are likely to consist of one or more of the following:
[Note On] Giving a MIDI Note number equating to a semitone, and perhaps using velocity as a volume parameter..
[Pitch bend] Which can either be high resolution (14 bit) or low resolution (7 bit)
[Volume] A master channel 7 bit volume value
[Other controller] any other available continuous controller, which can be either high resolution (14 bit) or low resolution (7 bit) and can be assigned to match a parameter on the reciever.
If the pitch-Midi interface is generating ONLY Note-on messages, and the reciever (Sound module) is not in tune with the Theremin, BUT this error is consistant, then it could be that:
1.) You are playing the Theremin 'sharp' by less than 50 cents, and the pitch-Midi converter is outputting the nearest Midi note number, which will cause your reciever to sound flat.
If you have no tuning function on the pitch-Midi, you will need to tune your reciever to the scale you want, and play the Theremin to that scale.
If your Pitch - Midi converter transmits both Note On AND Pitch bend, Then you will need to adjust the pitch bend sensitivity on your reciever (unless you can do it on the Pitch-Midi converter) so that the Theremin and reciever track correctly between semitone intervals... However.. This can be more difficult than it looks - all depends on what facilities the Pitch-Midi converter has, and how it interpolates data between intervals.. The relationship (curve) of both P->M and the reciever need to be the same to get perfect tracking.. They must both be linear or both be exponential.
The above also applies if the P->M transmits high resolution pitch-bend data, and this is the primary means of controlling the recievers pitch... There are few Midi Recievers which have a wide pitch-bend span.
MIDI from a Theremin is not easy to implement well, and MIDI is (in my opinion) only barely able to deal with Theremin output - To get the best from a Theremin-Midi setup, you really need a full understanding of both, and you need an external MIDI Merge box and MIDI controller so that you can 'tweek' the reciever for its best implementation of the data.. Ideally one has a high-end controller which allows, for example, one to add an offset to pitch bend data.
My work with MIDI leads me to believe that Voltage Control is a FAR better expansion method for Theremins.. However, I am doing MIDI on my Theremin because I Must - I now have an investor who insists that this must be included.. He may be right, he may be wrong - But it is a pain in the RS! In order