Sorry for the long wait for replies. I've left the jumpers in the position they shipped in, jltursan. They were (luckily) already set correctly.
The Dupont cables are temporary, but they fit fine for now. I am going to make a proper, short IDC ribbon cable for the USB module once I finish some other things.
Unfortunately I discovered I had accidentally swapped IC2 and IC3 on the audio/joystick board of the Micro-Expander set, and when trying to rework them I seriously damaged the board. "Goodbye, traces. We'll miss you! Don't forget to write!"
Part of me can't believe it took me so long to uncover the problem (lots of tracing, wondering why the machine would power on to a scrambled screen with the audio board attached, even if the AY-3-8910 chip was not present) when it was obvious even in the photos I shared here. In good news however, the soldering I had done all checked out, I have plenty more of the SMT chips, and another set of the Micro-Expander boards was only $20. I've already placed the order.
In the meantime, I have been using just the ROM/RAM/USB board and having a lot of fun loading images made on my PC onto the Aquarius, tinkering with some visual effects (Aquarius Demoscene anyone?) and some blocky scrolling, and keeping myself from getting discouraged. It occurs to me that games with very large and complex levels could be loaded off the USB drive and into 32K-36K of RAM.
It may be a while before I have everything back together (and I am trying to get my hands on a real mini-expander as well) but I will keep you all posted. This community makes me feel great, and this project has really upped my electronics skills even if I have made a flub or two. Cheers!