It's one of those downloads I've had for years, but isn't of much help when it's deeply buried along with hundreds of other files.
Well, I've solved the "Modem 2" and "Serial 2" port problems. Like many of the other MSTE problems I've had this was a frustrating/silly but cheap fix. I pulled out (thanks to a PLCC extractor tool which I've had much use for) the Z85C30 (a PLCC chip underneath the power supply) and this is what I found: Once the pins in the upper right hand corner (and other pins close to each other) were straightened out it worked a whole lot better! Using ConNect and selecting the appropriate ports I could now communicate with my STe on all three of those serial ports
So to answer my own question: U306 (MC68901) appears to control "Modem 1" while UA04 (Z85C30) appears to control "Modem 2" and "Serial 2".
I also gave the diagnostic cartridge a go, but the remote display still only worked with "Modem 1", so I guess that's the way it goes.
The SCC and serial tests still didn't work, so I assume there's a separate SCC loopback connector to be used -not the serial loopback connector I made. Does anyone have a pinout for it?

