Just make sure the frame is well supported on jack stands and level when you remove the crossmember, and when reinstalling the modified part. You'll also need to fabricate mounting points for the mid-engine mounts and a crossmember for the transmission tail shaft, so the only purpose for the dropped crossmember at the bellhousing area is to prevent frame flexing at the spring mounts. If you're doing a butcher job on the frame to install independent front suspension, the frame is probably going to get distorted anyway, no matter how many precautions you attempt.
Jerry
