I'm sure it's possible, especially with a flashing tool being provided to the dealers etc. As one of the users below stated, I would bet the files are similar to that of a car ECU, but I'm not sure. The main challenge will be a) Determine if the files come encrypted etc b) If they use a checksum to validate that the file is not corrupted (I expect they do so this will likely need to be recalculated c) Which is the most difficult part, what do the fields in the file actually mean. It sounds like you have access to the files and tool already, do you have a size of the file? I'm curious as to how complex it is and how they are mapping the fuel/tune etc. Are they interpolating on specific data points? Do they have set data and the saw leaps to the next "tune" depending on what the sensors are reading?
As you can tell I'm one of the rares you speak of but figuring out what's in the file AND how to use it is non-trivial. If you had multiple revisions of the file it would be easier to narrow down the format of the file assuming you knew the behavior differences with each file. Has anybody pulled the carb to see what CPU is running? It could be a starting point if it was a known processor and you could pull the ROM and de-compile it, at least into assembly language.
I used to build utilities that downloaded firmware to server adapters for a living so it's similar to what I've done before. Backwards engineering this would be a tad tougher.
I wish I had time to spend on it as it sounds like a fun project but working 60+hr a week plus maintaining a life is tough!