No, no, no, ...... no silicone gasket maker ..... ever ..... anywhere on the bike. When I find that on a bike I get, I know I may be in for trouble because the bike was worked on by a real rookie. That shit is just plain terrible. For gasket sealer on these, in the very few places it's needed, you want to use something like Hylomar or Yamabond. These are non-hardening sealers but not silicone. For the intake manifolds, I put a small bead on the manifold side, nothing on the engine side. This way, the gasket sticks to the manifold and comes off with it. Not like what you're faced with now, lol. You can use paint stripper to basically melt the old gaskets off. It will take several applications. Apply it and let it soak for 10 or 15 minutes then gently scrape off what has softened and re-apply. This is the safest way to get old stuck on gaskets off without damaging the sealing surface.
When you install the new manifolds, if possible let them sit on there overnight before putting the carbs on, then re-torque the mounting screws. This thick gasket will compress quite a bit so the screws will be pretty loose the next day.