Jeff,
Used to do this for a living so have a little background.
Where are the new off colored leaves coming from? Offshoots from the main branches or low on the trunk right by the ground?
If its down low on the ground then it could be coming from the "root stock" or base part of the tree. Many trees have a different root stock from their trunk.
Like this:
Anything growing from below the "knot" in the trunk is called a "sucker" and not wanted. The roots are picked from something hardy and strong, but usually not with good fruit.
Now, follow up the branches and see if on the main ones coming from the trunk if there is a sort of a break where it goes from the main stalk. This is where the graft was made on the tree. Anything from before the graft, in other words, on the main tree's trunk, is also not as good. You want fruit from the outer portion of the graft.
Any sprouts or growth coming from below the main graft or between the grafted on limbs and the trunk will not have fruit or the fruit will not be as good.
When you prune it the important thing is not to prune off any of the grafts. Prune "after the graft" but not too close to the graft. Give it a foot or so if its a mature tree but not too much more. It will grow behind the prune point and bush out from there.
More info on grafts here:
http://images.google.com/imgres?imgurl=http://www.extension.umn.edu/distribution/horticulture/images/0532_F07.GIF&imgrefurl=http://www.extension.umn.edu/distribution/horticulture/components/DG0532c.html&h=271&w=375&sz=8&hl=en&start=158&um=1&tbnid=EJCYprfhtaOLdM:&tbnh=88&tbnw=122&prev=/images%3Fq%3Dgrafted%2Bfruit%2Btree%26start%3D140% 26ndsp%3D20%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26rls%3Dorg.mozilla:en-US
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Also, where do you live? Many state universitys have a horticulture department who might have someone who could come out and help you. Worth looking at.
Hope this helps.
Joe