Yikes! First, I would depot the plant and inspect the roots and try my best to determine the extent of the damage. If the roots are sour smelling, black, slimy, you probably need to repot to save the tree. If, by chance, the roots appear ok, you could set the plant (out of the pot) on newspaper overnight so the soil mass can dry out, then return it to the pot. I can help you with more precise directions and some tricks that will help you keep the soil from getting too soggy again if the roots are ok. If it needs a repotting, we can address that as necessary, if you're willing to put the effort into it.

The insects in the soil are PROBABLY feeding on dead plant material. Hopefully, getting your watering habits and soil moisture levels under control will also bring the insect population under control. Let's see what you have to say about the condition of the roots & whether or not you want to make the effort to repot it if it needs it.

Best luck. ;o)

Al

What is the temperature in the room? Meyer lemon does not need high temps in the winter, just enough to keep it ticking over. Mine lives in a cool glazed porch in the winter where it flowers and awaits its trip back outdoors in March. It gets a little water when really dry and removal of dead leaves. I keep the surface of the soil scratched up a little so it doesn't compact and gates a bit of air. Also you need to watch out for scale which is worse when there is no wind and rain on the foliage.