Don't fret! As David mentioned, I've done the same thing... twice!
Okay- drilling the whole will work but it can be a bit messy with regard to wire routing.
Instead, here's my trick:
You have four wires (two from each battery pack) passing through the end cap to deliver power to the ROV. The wires are 18AWG so just two wires should be able to handle the current from both packs. If you splice the wires so that both packs are put in parallel outside the tube (I like to do the splice somewhere that will end up in the yellow sheathing so no one sees) you can use the other two for the tether.
Here's an awesome drawing I just did (apparently with with my left hand while blindfolded) in MS Paint showing what I'm talking about:
After you do the splice, you'll want to coat the solder junctions with several coats of liquid electrical tape (just like you did for the motors) and then cover that with heat shrink to keep the liquid electrical tape from wearing off with fatigue. You'll also need to rewire how things are connected to the molex connector. Here's a photo of how I rewired things for (one of) the ROVs I screwed up.
Let us know if this works out, and good luck!!