[Patrick]

What's the gearing in the MBX5T? Is it a similar final drive ratio to what you used in the revo? Overgearing can be one thing that causes cogging.
The mm software could help for sure, but if the same setup worked without cogging in the revo then I'd also look for things that could have changed when putting in the mugen, like the gearing, smoothness of the drive train, and that none of the plugs and connections are loose.