Need some guidance on transmission/flexplate/torque convertor

Yes, just use the flex plate from your 5.9 Magnum and slot one hole out so all 4 bolts will fit. I'd suggest holding the flex plate up against the converter while it is still out of the car, put the 3 bolts that will fit in, and then scribe the flex plate at the 4th hole where it needs elongated. After you get that one hole filed out to fit, then go ahead with the install. It should fit at any position you line it up, but being gun shy about converter bolts not lining up, I would mark both the flex plate and the converter at one bolt hole, put that one on the bottom when you start putting the bolts in and you will be sure all 4 line up right. Hope this helps.