I have a UR 10 equipped with a 85 gripper. A challenge I have ran into is currently we produce numerous parts that require hand stacking to prevent damage to critical features.  Currently, we stack them in a box about 27" by 28" by 13.5" deep. The issue becomes how to place the part accurately on the bottom of the box. Two issues arise, the first is interference of the wrist joints with the sides of the box and second using my current gripper I can't place them side by side. The parts are basically cylindrical with a hole thru the center. Some can be stood on end but most need to be laid on there side. Which seems to rule out gripping on the ID of the thru hole. How can I go about achieving this task?
 

@mertzga could you post some pictures of what the box looks like with the parts stacked in the box as you would like?

Here are two pictures. The one with just two in it are the actual parts I am working with. The other are components of my finished product but they depict how I need to stack my finished parts. Layered with cardboard between. I have been thinking about some type of vacuum gripping with extension to clear the box. I don't know much about payloads and whether I can pick on round parts:

@mertzga  a simple solution for the wrist interference would be to put an extension between the tool flange and the gripper so that the robot never goes inside the box.  Another option is to program the robot to "flip orientations" for different halves of the box (I have done this in the past using a custom written pallet program using count variables).

Also because these are not in nests, you could place the box onto a compound angle to make sure gravity pulls them all to one corner.  From there, and using the above ideas, you could use the robot's pallet routine with some extra IF logic, or use your own pallet routine to iterate through the box.

@mertzga you could use vacuum with the object, a compliant bellows cup should be able to pick the part. By using an extension as you thought and @Grady_Turner recommended you could easily reach in the box. This vacuum could also be used for stacking the cardboard sheet between the layers. 

@mertzga
I think the guys have really good ideas with longer tooling and suction cup tool or electromagnetic tool if your part can be picked using this kind of tool.
Concerning the program. I worked on this one below before (I added only the first part of it and this is not the final program as this is the one that I had in my UR Simulator before it was tested on the robot). I used a line pallet sequence to place a line of part across the a box. Then, once the first line has been placed I move on to the next one until the entire row of parts has been placed. This allows me to change robot tilting position as it is placing the lines across the box. So tilted in one direction for the first line and tilting all the way to the opposite position as it is moving across the box placing all the lines of parts. Also in the application I tilted the box a bit such that gravity would make parts stick to one another as I was stacking them. I had fewer parts then what you have so my program is a bit longer to do but it worked well.

Program
   BeforeStart
     boxLineID≔1
   Robot Program
     MoveL
       Gripper Open
       HomePos
       ApproachPick
       PickPosition
       Gripper Close
       ApproachPick
       HomePos
       Approach2Box
     If boxLineID≟1
       Pallet
         Pattern: Line
           StartPos_1
           EndPos_1
         PalletSequence
           AppPos2Drop1
           dropPos1
           Gripper Open
           AppPos2Drop1
         AfterEnd
           boxLineID≔boxLineID+1
     MoveL
       Approach2Box
       HomePos