OK, you have a few problems which are corrected in this sketch (I think, to be sure you need to breadboard the real circuit and make sure it works!)
Darkroom Timer2.fzz (67.5 KB)
Since I needed to make changes I re wired breadboard in a more readable form. First your 2 pin header is available from the generic header like this:
first drag the part in to the sketch then change the number of pins from 2 to 3 in Inspector like this
Here is the new sketch
Darkroom Timer2.fzz (67.5 KB)
With these changes/additions
First current limiting resistors on the segment lines, then pnp transistor drivers on the digit select lines which now go to I/O ports (as they need to be selected.) This display is multiplexed. That means that you write the 7 segment value to the digit, then select (by pulling the output port from the default all high to low on the digit you want to display) the appropriate digit then lights up in the correct place (with all 4 select ports grounded all digits would have lit the same and drawn too much current!) You then need to repeat this in your code on a regular basis (there should be examples in the arduino forums of how to do this!) As noted before all the current for all 7 segments flows through the select pin so that is what needs the transistor to protect the I/O port (which is limited to 40ma of output current.) Finally your three color led is common anode and thus needs to connect to 5V to operate (not ground.) I didn’t do anything about pcb at this point because you may want to move things there around. Another problem (that I don’t have a fix for) is that as it stands one or the other of the motors will always run. Because when the relay is powered off the NC to common connection (and thus the motor connected there) will run draining the battery. You need something like a power switch in the common line of the relay to be able to shut the battery off when not in use. As well are you intending to use batteries or do you want an AC power supply? There are generic AC powered supplies available in this forum post:
Hope this helps, if not feel free to ask further.
Peter