Well I have been having issues lately with bulk USB transfer to the atmega8u2. Seems after a few packets, the USB controller just stops functioning. I first thought maybe the entire MCU was crashing, but after doing some tests I found out that SPI connections would still function. Thought it could be a software issue, but all transfers work fine when using a atmega32u4 on a different board. I am currently waiting on new boards to come from the fab house. I tweaked the USB lines to folow differential pair routing, as well as tweak how the device is powered. Turns out the datasheet for that device is not that clear on how to power it how I want.

Here is a picture of the current device. I took the picture before I finished adding the 22ohm resistors for the USB though.