I am planning to pull three sets of four conductors (3 AWG wire) through 2" EMT conduit for a 30' length that is common to all three sets of wires, and then branch off at a listed metal junction box (10"x10"x4") to three 1 1/4" EMT conduits. I am doing this because I am planning to run wiring for three 100-amp subpanels from a 200-amp main.
I was not planning to make any mechanical connections inside of the junction box and just use the junction box to pull the wire through. Do I have to strip back insulation on the ground wires to make direct connections to the junction box?
250.4(A)(2),(3), & (4) says that "Normally noncurrent-carrying conductive materials enclosing electrical conductors or equipment" should be grounded and bonded. So while you may not have to connect the equipment grounding conductor to the box, the boxes do have to be grounded and bonded. Since you're using EMT, the boxes can be grounded and bonded via the conduit. If you were using nonmetallic conduit, you'd have to ground the boxes some how.
No, you do not have to attach a grounding wire directly to the metal enclosure if you are just using it as a pull point and you are otherwise grounding it using continuous runs of EMT. 250.148 from the NEC for grounding conductors to boxes only applies where conductors are spliced within a box, or terminated on equipment within or supported by a box.
From the 2011 NEC:
250.148 Continuity and Attachment of Equipment
Grounding Conductors to Boxes. Where circuit conductors
are spliced within a box, or terminated on equipment
within or supported by a box, any equipment grounding conductor(s) associated with those circuit conductors shall be connected
within the box or to the box with devices suitable for
the use in accordance with 250.148(A) through (E).
Exception: The equipment grounding conductor permitted
in 250.146(D) shall not be required to be connected to the
other equipment grounding conductors or to the box.
(A) Connections. Connections and splices shall be made
in accordance with 110.14(B) except that insulation shall
not be required.
(B) Grounding Continuity. The arrangement of grounding
connections shall be such that the disconnection or the
removal of a receptacle, luminaire, or other device fed from
the box does not interfere with or interrupt the grounding
(C) Metal Boxes. A connection shall be made between the
one or more equipment grounding conductors and a metal
box by means of a grounding screw that shall be used for
no other purpose, equipment listed for grounding, or a
listed grounding device.
(D) Nonmetallic Boxes. One or more equipment grounding
conductors brought into a nonmetallic outlet box shall
be arranged such that a connection can be made to any
fitting or device in that box requiring grounding.
(E) Solder. Connections depending solely on solder shall
not be used.