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From the photo there appears to be some minor pest activity but nothing extreme to worry too much about. I recommend that you adopt a preventive spray program with neem oil every two weeks. That will help to prevent pests and superficial disease like powdery mildew.

As for pruning, the top down view in this photo does not allow me to assess and recommend any branch pruning.

In future please confirm you location in the world, it helps us to give better information. I don't know what Apex means. Or is this a tech term?

Temperature, lack of sunlight and improper watering are common reasons for leaf drop.
This article will help you adjust the conditions for your Lemon Tree.
https://www.gardeningknowhow.com/edible/fruits/citrus/growing-citrus-trees-indoors.htm

Try not to spray the lemons directly, or use one of the many natural pest control methods to ensure that the lemons are safe to eat. As long as they are washed thoroughly, and there has been a couple of weeks between the time that it was sprayed and the time that it was harvested.

This collection of articles will give you ways to control pests, naturally, along with many other useful articles: https://www.gardeningknowhow.com/special/organic

Taste of fruit is best when plants have adequate nutrition, especially micro-nutrients and trace minerals, which most chemical fertilizers do not supply. Deficiencies develop over time from being used up by the plant and from leaching with watering and rain.

I recommend an application of COF (complete organic fertilizer) early spring, summer and fall. This is the best one that I know of:
http://www.soilminerals.com/Agricolas4-8-4_MainPage.htm

This is second best:
https://www.downtoearthfertilizer.com/products/blended_fertilizer/citrus-mix-6-3-3/

Deep water adequately but not too much.
Mulch the soil surface with compost.

If their urine or feces is getting into the container, then they are absolutely causing this. This will cause the burning tips from urea based nitrogen toxicity. I would recommend applying dolomitic lime to the soil to help drown out some of that nitrogen. It is good to apply this twice per year anyway, along with iron sulfate, and a citrus fertilizer.

Here is an article for more information on the care of container lemons: https://www.gardeningknowhow.com/edible/fruits/lemons/growing-lemon-trees-containers.htm

It is normal for Citrus trees to have thorns.
It's possible it will grow out of this thorny stage, but it will take time.

https://www.gardeningknowhow.com/edible/fruits/citrus/thorns-on-citrus-trees.htm

Your fruit issue could be results of growing conditions or actually could be fruit growing from the root stock. Root stock may be a variety that is not great in flavor.

You can try examining the base of the tree. If you have a visible graft line and the branches are below this graft; the top of your tree has died off. There would be now way to correct the fruit size or flavor. You would want to replace your tree in this case.

https://www.dpi.nsw.gov.au/agriculture/horticulture/citrus/content/crop-management/orchard-management-factsheets/garden