Im calibrating and fine-tuning my seedling (with many modifications) since weeks.
Im not using aluminium channel as guided rails, therefore I have different mountings. I use four ptfe blocks for guide my axis, and I screwed those blocks to the plastic. So it was straightforward to attach to this screws my pen holder.
But basically you want to drill some holes to the plastic and attache your tool to it, using screws. I recommend to attache another plastic and attache your tool to that plastic. So you can change each tool without drilling more and more holes.
Just a quick note: If you want to draw something using a pencil, you need less then 0.1mm precision on the Z axis. If not you cant raise the pencil and put it back on the paper reliably.
Drawing with the pencil is really helpful if you want to calibrate your cartesian bot.
If there is interest and you think it is helpful I can writeup my findings and improvements.