Sorry for the delay in responding. We have been keeping busy with the rewire project.
The Powerco was out yesterday, and they tested the neutral from the house to the transformer. They used a device that had some type of heater / fan in it(maybe for resistance on the line) when the line was dead, I suspect it was a type of megger. The test came out very clean.
I ended up on a speaker phone conference call with a lineman out at the house, someone in engineering and some really advanced high level engineer from the power co. We discussed the situation, and came to the conclusion that our neutral is just fine, and that with there system that 30%+ return on the water line is perfectly normal.
We also figured out that there is likely someone in the neighborhood that has a open neutral that is intermittently returning via our water pipes via our service neutral. That is why we didn't see it all the time, and that is why we ended up with the inaccurate readings (return currents that didn't add up.).
I will still take additional readings as stubbie suggested, thank you and will report back on those numbers. With the power companies assurances (and extensive testing, including re-doing the splices at the pole, checking the mast head butt splices, running a test devices on the meter for 24 hours and invloving multiple leves of the engineering depertment), and the fact that I am using NONE of the old wiring, only brand new work that I am making the connections on, so I am not too worried about it being an internal problem, doesn't seem too likely at this point. And based on what the senior enginer person told me, and what other have said, it sounds like it really isn't a problem at all now that we verified the service neutral is good.
I also pulled all the SE cables in the panel and in the meter socket, both sides, and make sure they looked good and put nolox on all of the wires.
I hope to get caught up with some more of the wiring project tommrow. I've keept my dad busy running conduit, pulling wires, stapling and routing wires in the ceiling. I've been fishing the wires and doing all the terminations. Just did a single box tongiht with 18 pieces of 12-2 in it. It was a bit daunting at first, but I made it very nice and neat.