I strongly suggest that you visit the Citrus Forum with your concerns. They will want details about your planting medium, temperature, etc. Pictures of the whole plant will be helpful, too. Not that you can't obtain some good help here, but the Citrus Forum is full of very experienced indoor citrus growers. I'd like to know from what part of the tree that that branch arose.

What kind of low temperatures are you getting right now? It needs to be outside if you are not having temperatures close to freezing. That will cure you leaf drop. Also your lemons are ripe. I dont know what kind it is or if they hold well on the tree but with just a few and that tree being smaller and having trouble I would remove them. Mike

When you do end up re-potting I'd use a slightly smaller pot it seems big for your tree but take a look at the rootball if it barly fills the pot go smaller if it mostly fills the pot just change the soil. I did the same thing with pot size with my first lemon, Put a tiny "stick" in a big pot thinking it would grow into it and would save me from from having to pot up as often. But it made watering really hard and ended up drowning my tree (also user error thinking my tree is dying it needs more water) Good luck! I think its neat you have a cool origin story for this tree and I am wishing you the best!

pip313: These haven't been fertilized. Fertilizer damage would have been more apparent when they were repotted in the new soil (if there was higher level of fertilizer with Miracle Gro) and wouldn't appear several months after being repotted. Vladimir: I haven't applied any fertilizer. I've only repotted them into the 3 gallon containers with miracle gro. OJ: Well, I am pretty further north so we get short days during the winter. This specific tree is genetically predisposed to produce giant leaves. The nodes are extended on the right branch that started growing less than a year ago. The main branch on the left is fine in terms of node spacing.