Keep the trunk you circled in red and cut the others off.

Poncirusguy the circled colors are blue.

This same pictures are in citrus trees in containers FB and the trunks were circled 1 in read and 1 in blue and stated that I thought the trunk in red should be kept.

I agree with Poncirusguy, that is the graft and take off anything below that line.

This is what it looks like overall, with two leads. i have since pruned off the deadwood. both leads are green, with new growth starting.

The one lead appears to be below the graft line and should be removed if that is indeed the case. It is my understanding that the root-plant isn't as desirable for production or eating as that which is grafted on to it. It has been my experience that the below-graft plant will take over, and that isn't what you want.

Citrus trees are bred for 1 of 2 purposes Great tasting fruit or great growing roots but not both.

But key lime does just fine on its own roots in containers. Mine won't stop blooming and bearing.

I believe that this is not a graft line, but was grown from a rooted cutting. I will grow it for a year to get it healthy again and consider air layering the more recent trunk and prune to standard shape next year. Thank you all for your knowledge and suggestions.

I reviewed your photos and that surely looks like a graft line. Unless you know absolutely otherwise, I'd suggest you treat it as such. The reason I say this is that what grows below the graft line will take over and steal nutients from the grafted one and it won't do as well as the ungrafted. The ungrafted rootstock probably has unsatisfactory fruit, which is why it's used as rootstock instead. I don't graft, but there are others here that can verify what I say.

Having said this.... the experiment is yours.