Thanks for the responses! More would be welcome too.
The Schneider controller is configurable to the Trojan battery profile. And I think that I did that correctly, although it might be a good idea to double check. But I did have that problem with the solar panel connector that wasn't letting the battery charge. So I've decided to try the Schneider again, but instead of powering it with the solar panels I'll feed it with an adjustable power supply set at the same voltage that the solar panels provided. BFL13, you make a good point about the electrolyte being different at the top than the bottom. That sure explains the difference between the voltmeter and hydrometer readings that I was seeing. I plan to do an equalization charge in the hope that that will mix things up a bit.