I think you should give the IS all technology they ever received, DHS, etc. Trying to balance the "Good" mechs against the "kinda shitty" mechs is going to be a ridiculous balancing hurdle, I'm guessing. And honestly that's all "Clan" and "IS" mean to me. I understand a lot of people are into the lore, but I've played Mechwarrior since the original DOS-based EGA version, the original Battletech PC games, and still wouldn't care one bit about what team I'm on, other than I don't want the "kinda shitty" mechs.
But, such is the idea, and I'm fine with it, I would just suggesting minimizing the balancing issues as much as possible by giving IS the most advanced tech it should feasibly have.