5.9 Magnum MPI swap flywheel idea

Why a 1/4"? Because that is as close as it comes to nesting? Is there material that could be removed to get it to nest without a 1/4" spacer?

I figure the flexplate doesn't need to be complete as it wont be carrying any load, it just needs to be strong enough to keep the tone ring stable at high rpms.

Yes, that is about as close as it comes to nesting. In the picture below you can see if you removed the edge of the flexplate it would sit closer, but there is still a gap there. You can also see in the second picture the one flywheel bolt that comes close.