The more i look at the last photo i see you problem you have the motor sitting in the wrong place. i'm not sure how it fits in a flux but the pinion doesn't sit that low in my truck, it really sits off the side of the truck even with the 44spur it don't look as if i could have a tvp wall on that side. pics blow but you can see how they keep the motor plate off the drivetrain.



EDIT !!!
swap the tvps then cut the rail out on motor side use the flux motor plate and mounts, run the integy roll bar that mounts from tranny to rear shock tower (i can't wait to get on or make one their stupid simple and works great) but this would keep things stiff and rigged.