Old thread I know, but I have the same issue as the OP with my 01/02 4runners. Rears were perfect length / fronts short, exactly as pictured.
I have the new low range ET (extra thread) nuts that I ended up not using. PM if you want them.
ET Style Lug Nuts for Wheel Spacers, M12-1.5, Set of 12
No issue on the 3/4" Bora spacers...plenty of thread engagement.
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Done - will give them a go. Engineering is sound with an ET nut.