Homebrew PCBs

I am working on CIS system now, before I was filling the cartridges with MIS ink. The auto-reset thing is new that I did last weekend. I modified the printer head height now it can accept up to 80mils (~2mm) board thickness. On the pictures board thickness was 31mils FR4 ( 0.8mm).
 Concerning alignment there was 2 problems for me 
 1- To be sure that printer is always starting at the same Y-axis 
  --- Open a slot on left side of tray and use slotted optical switch to detect it.  I assembled this optical switch to the left rear side paper entry of the printer. I modified my paper emulator software to use this sensor signal. 
 2- Alignment with my CNC.  
 ---Roughly estimate the position of the printed image on tray and put drilled PCB to this location and loosely fix it by Scotch. 
 ---Cover PCB with transparency and securely fix the transparency by Scotch. 
 ---Print your with via/holes unfilled image on transparency 
 ---Now, using small PCB sticks align the holes of the  PCB to the image on the transparency 
 ---Remove transparency 
 ---Reprint image with filled via/holes on PCB 
 Cheers,
 Volkan
  
 > ---the external tanks as well, or are you filling the containers?  I'm assuming external tanks since you're talking about reset chips. 
 >----how you did the alignment on them.  Also are you using standard thickness boards??