I was working on something like this for the toshiba tcd2304(?) units a few years ago. I have a working prototype in my closet using a psoc5.
Psoc5 is perfect for this kind of project because it integrates cpld-like functionality with a microcontroller that can also perform serial over USB. You you can get jitter free logic signals to the linear ccd.
The raman spectrometer functionality of these units could be really useful for certain projects. I have half a dozen of them in my basement, and I hacked them a few years ago just for the spectrometer portion. But the filters and fiber laser are nice too. But like you, I never really took it any farther, mostly for lack of a good project to use it on.