What are you trying to do here? Attach the cross member to the frame? I'd get everything mounted into place (with the cross member clamped to the frame) and then drill through both pieces of steel in place.
Or are you talking about getting the transmission mounted to the cross member? In that case, I grabbed a piece of scrap that I had lying around and modified it to fit the gap that I had. There are lots of ways to fab up a mount, and some are definitely better than others.
I think I need pictures to understand what you're doing.