If it were my tree I would not have pruned it so hard. I definitely would have left some of the upper branches as scaffolds to start with. But, since time can't be turned back, what I would do now is to remove a small piece of bark above spots where there are living buds. In your third photo just below the lower branch it looks like there is a small bud forming right there. About a quarter of an inch above that stubbed off branch, remove a sliver of just wider than the branch socket and deep enough to remove the cambium layer. The sliver of bark doesn't need to be very wide, just enough interrupt the flow of sap up from the bud area. That will stimulate the bud to act more like an apex bud and to grow. It worked really well with a couple buds on young trees this year for me that didn't seem like they were going to push growth out of areas I wanted growth to start scaffolds from.

Hard to say for sure by just a close up photo. I would snip off some of the leaves, stick them in a ziplock bag, and take it to a local nursery professional. You may need to call around if you don't know of a local nursery with trained pros on staff.

Hey guys, I have two dwarf Goldmine Nectarine trees with the same problem. (These are definitely Nectarine trees, not Almonds. I have both, and the two look nothing alike. Nectarines bloom hot pink, Almonds bloom white, completely different bark, and Nectarines have much longer curved and darker green leaves). Anyway, these trees are about 7 yrs old and nice looking trees, very prolific with early spring fruit which I thin down to about one per 8"-12" of branch length when they are grape sized or so. For two years in a row (about three and four years ago) one tree produced very normal tasty edible ripe Nectarines. Since then, it has been nothing but normal looking 1-1/2" diameter green hard fruit which stays green on the trees until fall and needs to be pulled off or it will rot on the tree during the winter months. Since I have two nice dwarf Bonanza Peaches and five various dwarf Cherry trees, which all produce beautifully every year directly adjacent to the Nectarines, this indicates that it is definitely a problem with the trees, and probably this particular strain. It is disappointing, but since I have researched this to exhaustion and the real reasons for this non-ripening are still just speculation, as well as limited space keeping me in the dwarf trees, I am yanking the Nectarines this fall and adding more Peaches rather than taking a chance on wasting another several years on more dwarf Nectarines. If you all have other fruits which do well for you, you may want to consider going with more of what you know works, or if you really want Nectarines, trying another strain.

====> "i dont understand how pruning the canopy .. will change the trees genetic predisposition to growing roots ... " Basically I wasn't sure because I was thinking if you keep the tree shorter and well pruned, I would assume it wouldn't need as many nutrients as it would if it were 1/3 bigger or whatever with a lot more branches, hence it wouldn't need to grow as large of a root structure to maintain the tree's needs; so I would think it possible that it wouldn't waste energy growing more/longer roots than it needs. That was my thought process anyways, apparently wrong? ====>"what's the native soil ... how old is the septic system ... " The soil is fairly compact, not sandy at all, and is surprisingly rocky once I got to digging a little. This isn't apparent from what's on top, which reveals no rocks anywhere until about 4-6 inches deep, just grass on dirt. I live in the PNW at the base of the Cascade Mountains so get quite a lot of rain, though summers are generally very sunny. I don't seem to have to water my lawn more than once or twice late in the summer to keep it green as at least once a week during the summer there will be a good heavy downpour followed by lots of sun most of the rest of the days (based on last summer). The septic field is pretty new (3 years old, only used so far for 2 years and lightly for the year I've been here, as it's just my wife and I, yet is a field/tank for a 4 bedroom, 4 bath house, despite the house being just 3 bedroom and 2.5 bath). The holes I have marked out now have the two closest trees to the field being a semi-dwarf santa rosa plum at 18 feet from the start of the field, then a Garden Prince Almond (dwarf, 10-12 ft max supposedly) about 30 ft from the field, then everything else (2 honeycrisp apples, 3-1 pear, goldmine nectarine, red baron peach, 1 plumcot, and 1 arbequina olive, 4-1 cherry) will be about 40-50 feet from the field, with most having a projected max height of 15-25 ft without pruning. Oh, and technically the olive will be about 25 ft from the actual septic tank itself (a 3 tank system clustered together), but I'm guessing, unless the tanks have an existing leak which I doubt with it being so new, the tree roots can't effect this? Does that seem safe enough?