Interesting timing on this. A couple of hours ago I sent Colin an E-mail suggesting that he address this issue in the instructions.
If you want to add sensors outside the E-chassis, you're going to need spare wires going through the potting. One of the things we're about to start playing with at OpenROV HQ is an externally-mounted I2C depth sensor, which will take 4 extra wires- power, ground, data, and clock. In a pinch you could do it with 3, by stealing the ground connection from the battery tubes.
I'm at the same spot as you in construction of the ROV, and hope to be potting stuff tomorrow. For my endcaps, I'm going to try to pot in 5 extra wires, so that every slot in the Molex connector is filled. 4 of these will be for external sensors as mentioned above, with one spare wire. For the hookups to the Molex connector, I'm going to have it fit the pinout used on the Power Distribution Board schematics (see here). The 5 extra wires won't be carrying a lot of current, so I'm just going to snip off some of the tether wire and use that.
I can only think of two downsides to adding the additional wires:
1.) The wire bundle needs to fit loosely enough through the hole in the endcap to allow the epoxy to flow and seal around all the individual wires.
2.) For the spare wires, I'm going to use some of the liquid electrical tape stuff on the exposed end of the wire, to keep water from wicking up between the wire and its insulation. Once the spare wires are hooked to a sensor, it will be sealed as needed.
Hope this helps. I'd certainly like to hear what others have done.