1)  No, not necessarily – if you want to fine tweak volume levels/velocity response etc you would still choose the specific articulation you wanted to change and select ‘edit articulation only’. 
 
2) Did you tweak the response curves in your TD-20 or just sensitivity settings?  The response curves should help you get closer to the response you desire.  Other than that reducing the Vel ctrl limit in S2 will stop the highest velocity hits being played which as you’ve found may be better for you.  You could also try playing with the soft and hard vel ctrls.  Bringing the hard velocity down will mean that you will have to hit the pad less hard for the higher velocity samples to sound.  Bringing up the soft vel limit will mean that the lower vel samples are triggered over a wider range and you will have to hit the pad harder to move into the gradient samples.
 
3)  Each velocity layer has a number of samples recorded which are cycled through to avoid the ‘machine gun effect’.  If you want to access all the available samples you need to set each value to ‘-‘ this would give most variation at the expense of slightly more RAM used.  If you want to limit resources used then reduce the number .  Bear in mind though if they are set to low you ar more likely to hear machine gunning.  By selecting ‘0’ you can actually turn an articulation off – this can be used if there are unnecessary samples loaded ie. for edrummers the flams and roll articulations aren’t much use.
 
4)  It is quite difficult to achieve cymbal crescendos as you describe.  A suggestion might be to load an x-drum of the same cymbal and use the envelope feature to slow the attack.  You could then have the x-drum assigned to the bow of your cymbal and the regular articulation to the edge.  I appreciate this would mean a change in playing technique but at the moment this is the only workaround I can think of.