Greg, are we having fun yet? I think your doing a great job, this stuff isn't as easy as some people lead a guy to believe, is it?
As I understand, you are faced with lowering the MII crossmember so the tie rods would clear the tubing inside the frame rail. Now, because the lower control arms bolt to that crossmember, because you are concerned about the ride height?

Two things come to mind. 1) Since the tubing is extra reinforcing, can you put a notch in the tube, and box it back in so the tie rods clear, without lowering the crossmember? You can probably notch away almost 1/2 the vertical wall height on both sides of the tube without compromising the strength as long as the tube is not the only structure there, and you box the notch back in with at least 1/8" wall material and fully weld.
2) Another possible option is to move the mounting holes for the lower control arm higher in the crossmember, you may have to trim the crossmember for additional clearance for the control arm swing. I suggest this one because many MII setups only have 1/2 of the control arm mounted to the crossmember, and the other 1/2 is attached to the frame rail. Maybe a combination of these two options would work better, or maybe neither will work. These things are hard to figure when you can't look at the real thing. Keep at it, you will get there. Gene