Calibrating steps/order
How to Calibrate. Oh man that is a good 2-3 page long blog post.. So I will try to give you the bullet point section. 

High level


Mechanical 
Firmware 
Software
repeat


Mechanical
Level everything. Bed. The X axis. Make sure there is no binding, etc. Also make sure the surface you are on is flat before leveling the printer by it.

Firmware
Get that printer moving. This is where you do you Steps per MM. I like Triffids guide.

Now is when you go into the software and start setting your slicer settings. This includes your filament measurements etc. You should go back 2-3 times between this step and the previous to make sure your extruding EXACTLY what you think you are. As mentioned by others filament calculation is hard. You need to measure across a lot of material. Take the averages. You will never get it perfect as the plastic is never perfect. Picking a solid supplier is a factor here too. 

Once you think you have that all working. Repeat. Start at step one. 

After your done looping though you will start with the slicer calibrations. Which is the meat of your question. You will take collections like this one or this one and tweak settings until you can pass each test. Do your tests in this order


single wall test
hollow cube
solid cube Here is a Bonus solid cube
bridging test (honestly I rarely do this one..) 
part fitting test


Now for testing when switching material. Honestly its best to start with their settings, and tweak them. I like to have a spread sheet of xy speed, Z lift, temps. Massage it till you are happy. The firmware settings like jerk and acceleration will be less of a factor between materials. Get it perfect once and don't touch it (till you decide it is not perfect).

You will be testing the new material with the same STLs as I mentioned in the precious section. You also might want to look into Simplify 3d (no affiliation) if you get really into it. Also SAVE THE SETTINGS. Nothing sucks more then losing all this work and having to recreate these profiles for materials. Do not trust slic3r to back them up, or to not randomly delete them. Hard lesson there.

Far as max speeds and accelleration..

Max speed will really be a function of how fast can you hear up plastic. If you have a e3d with Volcano mod you can really crank the speed up. So you go to the point where your extruder just cannot hit target temps AND you are unable to print solid infill. Far as acceleration and jerk. When you knock your extruder causing your print to shift, then you know it is accelerating / jerking too hard.

Best of luck! Let me know if I can clear up a section for you.