You seem to have confused yourself a bit, but yes it does sometimes take some digging to find every part of the story (I think that means the writers are doing things right)
I came in after the Clan Invasion, so I can't recall a period before hand. After the Clans things weren't getting confusing, just over powered.....Mechs just kept getting bigger and stronger, until finally we had the Fafnir walking around with two Heavy Gauss Rifles. Whats more it got to the point where Mercenary units were incredibly powerful and had access to these powerful 'Mechs. I applaud the writers for the Jihad and the global reset button to technology offset this.
As for the Jags, they cease to exist as an organized force. Any survivors have been picked up by other clans or escaped to become pirates.......there are files on an unaccounted for Jaguar Warship though....
Task Force Serpent left a detachment of the Eridani Light Horse on Huntress after destroying the Jaguars, the other continued on to Strana Mechty behind Victor Steiner-Davion and took on the Clans on their own terms through trials, as I'm sure you know. After beating them at their own game and scaring the Clans they headed home.....where Victor found his life turned upside down.
And the current plastic Clicky-tech minis are not replacements for the metal miniatures. They are a completely different game taking place in the same universe at a different point in time then the current Classic Battletech timeline. However the Classic Battletech Universe is slowly making their way towards this timeline.
Armourcast has lost or relinquished their rights to the Battletech line as far as I know. Hope that answers some questions
