Manual timeline starting from hour, minute etc misaligns with cells

The time headers follow the "groupBy" specification. If you use groupBy: "Day" the time headers cells with start at 00:00 and end at 24:00 (00:00 the next day). In this case, it doesn't depend on the grid cells.

If you want the headers to match the grid cells you need to use groupBy: "Cell".

See also:
https://doc.daypilot.org/scheduler/time-header-groups/

Let me know if it doesn't help.

I dont really understand what you mean.
I have a fiddle here, maybe you can show here:
http://jsfiddle.net/js29bcu0/

See the timeHeaders definition on line 10:

dps.timeHeaders = [{ groupBy: "Year"  }, { groupBy: "Month"  }, { groupBy: "Week"  }, { groupBy: "Cell" , format: "d" }];

Updated fiddle:
http://jsfiddle.net/g3c05pv2/

If I add another level to the timeheaders:
dps.timeHeaders = [{ groupBy: "Year" }, { groupBy: "Month" }, { groupBy: "Week" }, { groupBy: "Day" , format: "d" }, { groupBy: "Cell" , format: "tt" }];

and set cellDuration to 1440 then yes, the lowest timeheader and grid-cells align. But then the timeheader cell row misaligns with the other timeheader rows.

I tried the link you posted, but then the cell-row misaligns with the rest of the headers.

It can either align with the official calendar (groupBy values of "Day", "Week", etc.) or with the custom time cells. There is no way to change the week start to a specific hour of day (in the headers).

I find this kind of cell arrangement a bit confusing. The cell start doesn't really mean anything.

I would recommend a different approach: Make the first timeline cell partial (starting at current time and ending at midnight) and use "width" property to make it proportionally narrower, then continue with standard days starting and ending at midnight. The last cell can also be partial, starting at midnight and ending at the current time.

This way it will be obvious that the Scheduler displays just a part of the first and last day while the other cells will be standard.