I would remove the offensive branches. They will just become larger as the tree gets older. Do it in the spring so the tree can adjust better.

I would remove it ASAP too. The tree will adjust fine,

Echo.. cut. asap. Your lemon tree will be far better off. The only case that i could think of that would cause me to delay is a severe frost/freeze that would damage the cut zone. I don't think you have to worry about that in San Mateo the rest of this season.

It is done. Now it’s up to the tree to react to the exposure and put out new growth to cover the exposed bark. I’m hoping the two front branches aren’t also from the root stock. The leaves look normal and there producing a lot of the regular lemons.

Well done! Time to make lemon drops.

The graft line is obvious. Rootstock bark is darker than scion. You will need to watch for new rootstock shoots growing from around the cut. Over here builder's lime is traditionally used to stop rootstock putting out new shoots.

BTW, since trifoliate rootstock was mentioned above. That was no trifoliate rootstock. Maybe rough lemon or similar.

Some people recommend using a tree paint or wax to cover the wound while the tree heals itself, to protect from insect damage. That’s a pretty large cut, so you might want to think about it. Since I don’t have outdoor trees, I’m not experienced

Wound pain was once thought to be beneficial, however it is now known that it is best NOT to apply a wound paint covering. Let the tree heal itself.

The trimmed tree looks great.

I’ve heard by the time you put the wound paint on fungus/bacteria have already landed on the wound and painting over creates a nice moist environment for them to multiply.