If you're doing the swap in stages (meaning, having the 351 for a while until you get to your stroker), you'd need an ECU for a manual transmission, until the engine and Sniper go in.
But as BB said, you can put the 5 speed in now, and complete the swap, work the kinks out, etc. etc. and then later when you find a ZF5, it's a direct swap. Pop the M5OD-R2 out and put the ZF5 in its place. They're the same bolt pattern and dimensions, as long as the ZF5 is for a 4x4 small block.
But as BB said, you can put the 5 speed in now, and complete the swap, work the kinks out, etc. etc. and then later when you find a ZF5, it's a direct swap. Pop the M5OD-R2 out and put the ZF5 in its place. They're the same bolt pattern and dimensions, as long as the ZF5 is for a 4x4 small block.