RE Issue 2. If using Mach then I would look to using a brain or macro pump.
If used in combination with G0/G1 and G4 (Dwell) (which you could easily make your CAM program insert G4 by altering/making the post processor special for this job type) and setting the dwell time needed to dispense the correct amount of paste. Then building a simple macro pump set to watch when the X & Y axis are NOT moving which then triggers your output connected to the switch.

Could go some thing like this. G1 X11,Y20 F900 G4 P2 (pause 2 seconds) the Brain will see this pause then turn the pump ON untill either X or Y axis start moving again or set amount of time which you can set in the brain.

There will probably be other simpler ways but I'm pritty sure you'll end up using either a bit of VB in a macro or a brain. Macros and brains are very powerfull and can really make your machine do pritty much anything you want.

RE Issue 1,

Dont the smd chips come on tape or strips that have pre-determined spacing.? If not then build a special holding jig that you know the coord's of the centre of each bay.?