Yeah, just to reiterate, your itinerary for the endgame is:

-> Virmire
-> On rails section in a location (I won't spoil where, though)

-> Free roaming

----Point of no Return----

-> Ilos
-> Final Mission


After the on-rails section, you're back in the Normandy. As long as you don't head to Ilos, you're golden. The Turian insignias and Salarian medallions don't have an effect on any quest in ME: 2 and ME: 3, but they might influence an achievement or something. I'd try and get them regardless, just to say you've done everything and you are close, but without a guide, it'll be a bit of a slog.