Almond Seedlings -- problems with acid soil?

Last year I moved from Utah (5000 feet, alkaline soil, 12-15 inches of water per year) to south central Kansas, and am now building a home on 3 acres of heavy clay loam, acid soil, 30+ inches of water per year, 1000 feet.

I started a bunch of trees from seeds I brought with me, mostly from my old yard. Started in the soil I have here, no amendments. Apples, peaches and apricots seem to be doing great, even the cherries, which was surprising.

Almonds, not so much.

While many germinate in the refrigerator,  most do not survive transplant. Four survived transplant in the first batch. 10 survived of the second batch, but many are struggling.

One sags with any level of heat. Another came up with no seed leaves, but I think that one might be transplant damage. Many are growing their leaves down along the stem, not drooping, but actually growing downward. One came up nearly yellow.

The older trees seem to have a number of nutrient deficiencies, in a pattern I haven't sorted out yet.

None of the other trees seem to be affected. Only the almonds.

Could this be the effect of acid soil? I haven't been able to find a real chart of nutrient deficiencies based on ph. Lots of articles,  but they don't give me the information I need.