[MachinePipeliner] Fix Phi generation failure for large stages

The previous code overwrites VRMap for prologue stages during Phi
generation if a register spans many stages.
As a result, the wrong register is used as the one coming from
the prologue in Phis at later stages. (A process exists to correct
this, but it does not work in all cases.)
In addition, VRMap for prologue must be preserved until addBranches().

This patch fixes them by separating the map for Phis into a different
variable (VRMapPhi).

Reviewed By: bcahoon

Differential Revision: https://reviews.llvm.org/D127840