The branch with the red arrow is the scion. So even though the rootstock is about 75% of the tree, I should cut it back all the way to the base of the scion?

As long as you can positively ID that branch as the scion, cut all the rest back to the base of the scion. It's hard to tell from the picture though, was hoping for a more definitive graft line. More like this.

Evan

The scion is fruit-producing correct?

Yes, the scion is unifoliate and is fruit-producing. The trifoliate (three leaflets) is the rootstock which will quickly overwhelm your scion. Remove all rootstock (trifoliate) branches as far down as you can. Keep an eye out for new rootstock growth and rub off, should it appear. All the trifoliate should be doing it supporting the scion and providing the 'roots' for it.

I have a similar situation. In my case it seams the wanted tree was satsuma. But someone has cut back the satsuma branches down to two or three small branches. The trileaf branches or 99% of the tree it is about 13 ft tall and full of small perfectly round fruit on the trileaf branches. Only about 4 satsumas. Will the fruit on the trileaf branches be any good?

Curently satsumas are ripe and good the other fruit is between yellow and orange and sort of green inside and when cut open kinda smells bad.

What should I do?

corey: As in all cases where rootstock is allowed to grow -- it must be removed to the main trunk. Otherwise it's a waste of energy to be supporting nasty fruit. Unless for some reason you like the bad-smelling fruit.

Ok thanks, I wasn't sure at this point if it would be salvageable. I also did not know weather the tri-leaf fruit was just not ripe yet. Never had fruit trees before. Thanks again!