first time I've noticed (but still a bit difficult from the photos) - for some reason in Aus the regs (of which we have many and often don't know why) have the main sub-frame beams at least partly over the chassis rails. I also notice that the three (?) sub-frame mounts seem to be at the extremities. Its quite possible that the original unconstrained chassis rails were oscillating (bending) more than with most designs, resonating even, which may have led to the fatigue cracking of the chassis rails.
From reading so far the new chassis rails are of different thickness and will resonate differently (a bit like the bass notes on a piano are thicker heavier (and longer) than the high notes).
One possible suggestion could be the addition of extra flexible mounts. Simply springs which are rated to support their load when compressed a bit and long enough that they don't change much over the limited range of compression/expansion. Extra support for the sub-frame, but also some damping for the chassis rails. There's "lots" of other possibilities.
Very difficult without being there so treat this as possible ramblings of deranged mind .....