Your grammar is correct, however it sounds a little confusing, that's all.
I completed three major tasks. However/Although, the most important project I did/finished was that I obtained a diffraction-limited configuration for the/a SS-OCT system.
Unfortunately I have no idea what the topic is - diffraction-limited configuration for an SS-OCT system, if I knew what that was or the context that this situation was in I could help further.
Your grammar is good, there needs to be either a definite "the" or indefinite "an" article before SS-OCT. If you have mentioned it before and the listener will understand what your referring to, then it is "the" otherwise use "an"