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How were firmware values chosen
Can luc or someone explain how some of the defaults were chosen for the firmware? Things like the max acceleration values and speeds.

What about the pitch of the drive rods? I assume those were just measured.

I'm still very new to 3d printing, but I want to understand if there are general guidelines and what they are. I'd also like to understand the things which are unique to the davinci.

Any books/articles I should look at?

All values where done before I handle FW - I just changed Z acceleration as was too noisy - and tweaked the Thermistor tables because having some issues

When I started 6 month ago arduino and 3D printing, I have read everything I can found on internet about subject, and also read all documentation of Repetier FW as it describe a lot of settings very well..
I googled every terms/name, study all flavor of GCODE , and read marlin / repertier github and issue tracker as most of the time it helps you to understand what is not documented.
More you read, more you learn, more you know you don't know

I am not sure on which forum I can answer this question, but I suspect, in any event, that you are the right person to answer.

I am using Repetier-Host v1.0.6 and I am printing a file called "bigspool-hanger.stl".

If I look at the generated G-code after slicing, I see the beginning of the file that looks like this:

; generated by Slic3r 1.1.7 on 2015-04-09 at 19:16:13

; perimeters extrusion width = 0.50mm
; infill extrusion width = 0.52mm
; solid infill extrusion width = 0.52mm
; top infill extrusion width = 0.52mm

G21 ; set units to millimeters
M190 S105 ; wait for bed temperature to be reached
M104 S200 ; set temperature
G28 ; home all axes
G1 Z5 F5000 ; lift nozzle

M109 S200 ; wait for temperature to be reached
G90 ; use absolute coordinates
G92 E0
M82 ; use absolute distances for extrusion
G1 F1800.000 E-1.00000
G92 E0
G1 Z0.350 F7800.000
G1 X51.321 Y48.443 F7800.000
G1 E1.00000 F1800.000
G1 X53.268 Y47.221 E1.21982 F1080.000
G1 X55.781 Y46.728 E1.46465

Three questions:

1. Where do the values for the temperatures come from? I assume that they are taken from the Printer Settings dialog.

2. The sequence of the actual header commands looks pretty well the same every time. Is there a template file that contains that G-code that is tacked on the front of every file that I can modify to have my own sequence of commands?

3. If I create a Start Code g-code script and enter commands, will it be tacked on before these commands (and therefore will be altered by the standard commands making it useless) or will it replace the header?

I was looking at your simplified g-code for start and end and generally agree with your sequence. I would like to use that sequence rather than the sequence that Slicer uses. How do I do that.

Similarly for the end sequence. For example, I would like to turn out the lights and put the printer to sleep after a print is complete!
And I like the messages that you put out to the printer that would make the whole process easier. I also want to put the bed down to the bottom. I know all the codes required to do this, the question is being able to get rid of what slicer id appending at the end and sticking my own stuff there.

Any help or guidance would be appreciated.

all is about start /end gcode of your slicer and settings of your slicer (temperature, speed, etc...) you can do anything you want

I do not know about latest version of slic3r but I remember temperature behaviour can be only customized in cura / S3D (automaticaly I mean, you always can edit the GCODE) ,for example you can choose if heat bed first then extruder or all together in custom start, check here does not mention it

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