To your original question:
If I read this right. Truck has no motor or trans. You want to mock up a new motor and trans. If you intend to cherry pick sling/jack stand and block the new stuff in there to design the motor and trans mounts, you can remove the crossmember without any worries. You can design, build and tack weld (and maybe finish weld) the various mounts while motor and trans are mocked in place, if you wish as long as new motor/trans are not "loaded" onto the frame per se. You will want to measure the exact dimension between frame rails before removing the crossmember to observe any slight change afterwards. (probably none)
To the "new" crossmember phase:
I hope you are looking at those universal tubular motor and trans mount crossmembers. I like to use those.
Example1Example2Example3Your idea of modifying the existing crossmember may need some engineering thought/advise. Not sure if you mean for the tranny or the motor. Modifying/dropping existing crossmember may not be advisable strength wise. Probably best to derivet the crossmember and use above linked or equivalent. I have used them several times on 55-59. 350's, 454's and TH350. If there is some special reason they won't work on AD, learn me. I have also used an existing crossmember with mods. I am a Mechanical Design Engineer FWIW, like Kevin. I would also probably go with Mike's deal. It has a lot of bolts and hard to design. If you want to hear why my linked crossmembers are cheaper, better, easier, faster, better looking and more accurate. Let me know. If you wish to do a modification to the existing, maybe I and others can help but would have to see pics/drawing of the idea. All of us are just giving you input. Only opinions.
