on the PCB side there are a lot of things i don't understand, but lets walk through a few of them..
1) Layerstack.. its a bit thin right now..
2) why top and bottom components, as far as I can see it is definitly possible to do top components only..
3) no fiducials.. If you want this produced by a manufacturing company they will ask for fiducials for pick and placement.
4) try and change the design to full smd (for elco and Clk, diodes.)
5) you really need to get your power traces from the board better routed the singel source pin has a lot of 0.2mm tracks which i would increase...
also try an create a plane to attach to instead of traces from component to component.. now noise will be a massive impact on you design.
6) re update your PCB from the schematics...(when updating PCB from schematic there were a lot of differences still not done)
7) recheck design..and redesign the board.. making it like this it will not work..
don't get me wrong, its a good start but to get this ready for manufacturing you are going to do a bit more work..
typically i design even simple boards multiple times.. even though your netlist is complete its important to always look at your design and think can I do this even better... just save a copy in between and try thing out.. think like.. what if i rotate this component or.. does this connector need to be on this side??...
or if my optocouplers are the "gateways" between my connector and micro controller i should place them between the connector and the microprocessor.