. First, when you dramatically change the light conditions a Meyer will drop most, if not all its leaves, to replace them later with leaves better suited to the new light conditions. To move a Meyer from outside to inside without the leaf loss, you need to move it from full sun to partial sun for 2 weeks; then to full shade for 2 weeks; then indoors; reverse the process when putting it out in the Spring... and please DO put it out, if you can; you will be rewarded with a happy, healthy plant.
Second, when you bring it indoors to a sunny window, the plant gets warm; but the roots generally stay cool; and citrus roots don't like to grow into cool soil... the solution is to put some sort of heater to warm the soil, or to put the plant a little further from the window. The thing to remember is first the roots grow; and then the leaves and branches.
Don't stress about the flower/fruit drop; it is normal for a quite young tree; if you treat it well, you can expect to flower next in the Spring; and likely then it will keep some fruit, or too many fruit; be sure to post photos then, so we can help you.

Thanks for the advice about bringing the tree in, we actually just brought it in a few days ago because we had a cold night. As long as weather permits I'm gonna try putting it back outside in a lower light area before bringing it in for good, hopefully this will reduce the leaf loss.