Also, if I want to make a direct USB connection without the large cable ends, is there any problem with soldering the cores (and shield) of the USB cable to the pins of the Arduino's connector?
and I can see 50Hz at various points in my circuit
There's too much for me to digest at once and I can't comment much on the analogue/PSU stuff, but a couple of things I'm not sure about .
1307 GND connected to VBAT, its that OK. The chip will expect a battery on that to work when power is cut.
The 18B20 temp sensor, doesn't that need a VDD/VCC connection?
Silly question, but are you sure the external PSU is DC?
R5, 6 and 7 add up to 460.6k. Given that they are in series with a pot couldn't you just use a 470k?Admittedly the pot is only 2k, do you need that fine adjustment?______Rob