I've said this a few times but for the clan invasion give the clans IS Level 2 tech, let the IS be a little disadvantaged for a 30-day in-game invasion event, and then merge it all after the event.
That'll simulate the clan invasion, allow the clans to be initially technologically superior, and still maintain complete balance after the event is over and the IS gets bumped up to Level 2 tech.
As for omnimechs, they need to be converted to battlemechs and introduced that way. I said this in the OP very clearly. There's no point in using the TT's crit slot system as that makes every make an omnimech plus that system was made for building completely new and custom mechs. It was never really meant for modifying canon mechs. Many people don't understand that.
You are still ignoring the simplest balance option and that is assigning Battle Value to units in the game. It is how the TT game is balanced, and with some tweaking it could be adapted to work just as well in this iteration of the game.