Struggling with project. Not sure what to do.

[RoGeorge]

In my opinion, if the extra ramification traces were already cut, then it's probably the FTDI chip.
If the D+ and D- are not reversed, then it must be either a defective FTDI, or a fake FTDI that was bricked by the windows drivers.

[dmills]

Concur, 12Mb/s USB is not usually all that delicate.

Ground pours are better then thin traces, do them on BOTH sides of the board and via stitch extensively, still much worse then a nice solid plane, but better then what you have, and as said, think about current loops, they are key to anything high speed.

Vias are cheap, keep adding stitching until your board vendor starts putting the cost up because of too many vias,then back off just a little....

I would be very surprised if CircuitMaker cannot do at least 4 layers, that would make it basically useless for anything faster then audio.

Regards, Dan.

[stmdude]

Vias are cheap, keep adding stitching until your board vendor starts putting the cost up because of too many vias,then back off just a little....

Words to live by. 

[Jackster]

This looking better? No forks. Just via the FFC.
Bottom layer I covered with a GND polygon that auto fills. Removed most of the GND routes so that the polygon connects most of the GND components, vias etc.





[edit]
Not put a load of vias in yet. Working on USB first.