1. Bed set too high and would shift as a result
2. The carriage upgrade had bit of slack around the bearings and it could shift in the Y direction
3. My extruder has ~1mm of wobble where it will shift and stay. If it catches an edge of an internal wall it will show on that layer.

Fixes:
1. Lowered bed to rest at lowest point. Upgraded springs to apply more pressure to bed.
2. Used U-mold plastic to hold edges of bearings and take up any slack.
3. Printed a new base for the MK5 that has less wobble when using the E3D.

I figured I will post this here just in case this is the fix. Yes, I know this was an easy one. The simplest fixes are always the hardest.

just to be thorough, did you check the GCode to see if the shift was there? 

If you were to print this code again, would it repeat the shift in the same spot (same layers)?

Good question! I was actually planning on running through the g-code and doing min and max y value search and seeing how many times each shows up. It it doesn't equal my layer count -1 then that could be my problem.

I an running the print again but I won't be back until later tonight to see the results.

If you were to print this code again, would it repeat the shift in the same spot (same layers)?

Just out of curiosity is it shifted or indented all the way around?
If you can't figure it out where does that leave the rest of us?
unrelated to this issue I noticed on another post you have a spare chip you'd be willing to sell.
I'd be interested but I am unsure what that gains me? As I too am addicted to mods just not at your level yet.=D

It is shifted, where one side juts out the other side indents And there are plenty of smart people on here that can help out. I was hoping to find a resolution publicly so when this topic gets marked as solved, everyone profits

About the chip:

If you have a new board, the chip won't gain you anything because it is for the sanguinlolololululuo. If you do have the Sanguinololu then it will allow you to add the Panelolu LCD with SD card. The ATmega644P that comes with the old board has 64K memory limit. This isn't enough load the firmware that supports the LCD. In fact, the normal firmware is around 58K so you don't have a lot of room left in memory for many feature adds. The new boards have plenty of space so no worries there.

If you aren't looking to add a bunch of features to your stock motherboard then you don't need a new chip. If you buy a Panelolu, the additional upgrade chip is usually only $8-10 more. The only reason to buy the chip separately is if you need a new chip because the old one is blown or because you are looking to add a bunch of code.

Note: This only seems to happen in the Y direction. The bands differ in height, severity and period although, they match on all cylinders.