Some final updates to ensure all scripts work and all files are named correctly after recent changes.

- Corrected naming of merged histogram files so that the measurement scripts can find and use them.
- Updated the runnning scripts in bin/, including naming the output logs so that they can be accessed properly by the later scripts.
- Small correction in what is output during the fit in tools/Fitting.py so that only what is necessary is printed out to the log file)
- Updates to 98_fit_cross_checks.py matching the other recent changes #78 and #81.