Vex,
Y axis is define to max limit round up divisible by 5 major lines. If your max limit round up is not fit with divisible 5 then you will experience that kind of figure.
Ex: if total unit is 5000 / 5 = 1000 each major lines round up = 1000 = 100% but if total unit is 4500 /5 = 900 each major line round up = 1000 = 88.9% next 111%

Vex,
If you are using Task Dependent Activity type then activity calendar is used and only single calendar can assigned to activity but if you use Resources Dependent activity type then activity calendar is ignored and use resource calendar. This will allow you multiple calendars define on each resource like on my sample post #4.

On your problem you need to use Resource Dependent activity and create two calendars, one for day shift and one for night shift.
Ex: 08:00AM-05:00PM dayshift
05:00PM-12:00AM nightshift
For activity calendar you can assign 08:00AM – 12:00AM or 24 hrs calendar.

For your resource you need to create resources for dayshift and nightshift
Ex: Welder_DS, cal = 08:00AM-05:00PM – dayshift
Welder_NS, cal = 05:00PM-12:00AM – nightshift
Rigger_DS, cal = 08:00AM-05:00PM – dayshift
Rigger_NS, cal = 05:00PM-12:00AM – nightshift
And soon…

You have to define max unit/time per Resources per Shift then assign both on one activity. When creating a histogram use a shift calendar and shift Time interval as per my example.

Hope this will help.

vex,
P6 graphics is more advance compare to P3. If using Shift calendar you have to use shift timescale also in order to show the histogram. Max unit/time (Limit) should be define.
See sample below:

Vex,
On new version of P6v7 Hours Per time period are now change to based on calendar assigned. If you select Calculate average per time period on Resource Profile Option, that should follow calendar settings.