I had a parts truck a long time ago that someone had taken the cross member out of. By the time I got it the frame was so badly tweaked that the stock cross member would not go back into place. There was substantial twist on both sides of the frame. Even with one side bolted back in and jacked into place, the other was twisted too far to line up the holes. It took a very large pipe wrench hooked the the frame and a second jack to get it even close. This was all with just a stock engine in a lowered truck.
I never tried to get an alignment on that truck, just sold it very cheap. From the look of the tires it came with, it was WAY out to begin with. I'd say keep the cross member. The frame will flex in that area without it.
I'd just weld a lowered extension onto the stock cross member then cut out the part that is intefering. That keeps the geometry exactly the same until the replacement section is already welded solid.
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95 Isuzu Trooper Daily Driver
86 Isuzu Trooper reliable backup
77 LUV 2wd stock beltway blaster (resting)
79 4x4 LUV project: 2.6L, 5spd, 31s (eventually)
MEPR: Man, my 4x4 makes all other LUVs look good