[yossarian19]

At this point, I would look at re-building the offending crossmember. Guys notch the frame to clear the axle tube when they lower the suspension. I think a similar approach, if you have any overhead space to work with before getting to the bed, would help.

If you don't have any space between cross member and bed (I'm a newbie, did I mention?) then your best bet is probably to lower the engine mounts, like you say.

I'd first take a look at notching out that cross member & adding steel as needed to keep it structurally sound.