Mark's fix and instructions worked perfectly. Since making the change, I've gone back to the MyDefrag 4.2.3 which was causing problems and it now works without causing the problem. Thanks Mark!
But now I'm perplexed. I have a working hypothesis that it was the moving of $MFT with the bad geometry stored on the NFTS volume that caused the problem -- perhaps calculating a different location based upon one geometry (either in the BPB or vdi's disk geometry). But if this were the case, why can I still boot using fixntldr.iso which I'm assuming would use the partition info to find $MFT. Perhaps it is further back that an adjustment to the MBR was done to point to the location of the partition and the calculation done with the bad geometry in the BPB was used, resulting in a new location being placed in the MBR even though the partition didn't move. I have more digging to do.
Thanks all for your help.