Well, if you could post a photo, you would get a lot better advice; but short of that you have probably made some of the classic Meyer lemon errors. 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.

Johnmerr,
Thank you for the input, I am attaching a photo of the tree as you suggested. We actually have it decently distanced from windows but in a very well lit spot in the house, but we did not realize the process of slowly acclimating it's light. As soon as the weather is warm enough with no fear of frosting or low temperatures, we will definitely be putting it back outside. Do you have any recommendations for humidity levels? It is very dry here in the winters, would it be wrong to use a humidifier near the tree?
Also, we have read that when the tree grows thorns, it means the tree has been stressed, is this true? Are thorns an indication that the tree is not doing well? Thank you again for your advice!

Most all lemons have thorns; usually the biggest grow when you are treating the tree too well. For my potted Meyers and my garden Meyers I nip off the thorns with my nail cutter; if not you will lose blood. I would definitely take off all those fruits now, to give the tree the chance to put its energy into new leaves and branches; your lemons are fully ripe now and good as they will get. If your tree were older/larger and not stressed, you could leave the fruit on the tree up to 4 months; but it won't get better, only more yellow on the outside and a little less juicy. As for temperatures, Meyers will survive down to 28 F; and as much as 10 degrees lower with a cover and a 100 watt bulb inside the cover.

Sorry, I didn't answer your question about the humidity. I would just mist the tree with a spray bottle once or twice per day; and if you get bugs, you can put the plant in the shower and give it a good bath once a week or so.

Thanks for the great advice! I have trimmed the thorns, picked the fruit, and got a heat source on the roots. I even saw three new leaves and two new blooms coming in, so I am feeling a lot more relieved! Thanks again!

John..Great info and thanks!

But remember that Citrus in a pot will NOT survive temps that low...I think you mean planted in the ground, right?

Mike:-)

Thanks, also having the same problem with leaves dropping. Have buds, 12 greenish lemons, small insects that look like gnats and stuff that looks like roots dug up...help!!

Forgot to add that I have an adjustable grow light for the lemon tree, tomatoes and garlic.

Sounds like your mix is staying way too wet far too long or just too much organic matter preventing the roots from taking in oxygen and nutrients correctly.

Couple pictures would help with diagnosis.