I have an EM with a 428 and have pulled the Lakewood/Tremec several times (unfortunately) but I do have removable tranny cross member. In fact, I am currently running an 11" Centerforce Dual Friction (#DF226033) clutch. When I first installed it, I thought I had the same problem, but after taking a break and coming back, I finally found the correct 6 bolt holes to use (many in the flywheel). Could this be your problem?
Here's a pic.
Gene