Congrats!
I´m on the same path, finished WC1 and Secret Missions 1.

Have fun and good luck! I think SM1 is the hardest in the series. Apart from the odd mission here and there, it's easier after that (although not easy).

the ending mission for one of the expansions for wc2 was the hardest to me had to destroy two cap ships that can one hit kill you

Yeah I'd agree that's the hardest individual mission (it's end of SO1), except "Save the Ralari" in WC1 but you don't have to beat that one.

Yeah, never managed to beat that one.

took me about 30 tries no lie, the problem is your wingmen shoot you more than they shoot the enemy

My problem was mostly that I got always destroyed before I could be close enough to launch the torpedoes because of course those guns were a one hit kill.

It doesn't help that it's almost impossible to tell if you are in the blind spot of these things (if they even have one, I was never able to tell), god I hate the sprites of these games, give me the stylized goraud shaded 3D models of X-wing and Tie Fighter anyday.

Just finished WC1 with both Secrets missions, now WC2 :)

You're allowed to fail the double Fraltrha mission too, you're sent back out on another mission where there's only one Fralthra and it doesn't effect the ending.