The tailshaft housing on the older 700R4s have a mounting location that is farther back on the housing than the newer 700R4s. This makes it so the crossmember won't block the rear bolts on your pan, and you can use a deep pan without having to trim the front edge of the crossmember.
I'd recommend removing the bolts that attach the crossmember to the chassis. Then install your transmission, and attach the transmission to the crossmember with the two mounting bolts. Make sure the crossmember is sitting perpendicular to and centered on the chassis. You can then mark the new chassis hole locations and drill away. This is way easier if your cab is off. If it's not, it'll be a challenge to drill the upper holes.
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