i would presume that by the jihad the Inner sphere C3 systems are easily useable with clan-tech weapon systems. after all by then the IS had captured enough clan weapons that their performance specs would be well known. C3 would mainly need to know the performance specs (the various factors that aggregate to create the range bands and modifiers in the rules), and adding new weapons should be as simple as a software patch with that data.
by the Jihad clantech is going to be well enough known that most systems will either already have it loaded in their software, or have access to software updates to add them.
if this was a game set during the clan invasion though you'd probably be out of luck, since the data needed would still need to be collected.
that said your GM should check the date your game is set at, and the intro dates for any hardware you captured.. anything introduced only 2-3 years prior would probably not be in the C3 system's software.