After making a few tests I figured out an easy way to fix the incompatibility between
Achim's timer for time lapse photography and my Nikon D3100 (I swear this fix would make the timer work on a D90 too).
I basically soldered the timer inside the remote shutter button, this way the PIC is able to capture straight away the focus and shoot triggers and then repeat for the future. Works like a charm :)
I decided to keep the jack plug soldered as there was enough room in the plastic case.
Another way around is to add one or two external buttons, you have to make it so the GND wire first touches the "focus" wire then then "shoot" wire and then they are released together.
To stop the timer (as Achim says), just press the button halfway to hit the "focus" wire but don't hit the "shoot" wire, wait a few seconds and it'll shop running :)