As I mentioned, I don't remember seeing the alarms you described as caused by the BIOS/batteries although I suppose it is possible if it was partially corrupted this could happen. However, if I am remembering correctly, even when the RT board is completely dead, the KTI will still pass the diagnostics, so seems likely that is unrelated and you are looking at a couple separate issues. The fact that you changed the RT Battery also makes the RT board suspect even though it is passing the diagnostics.

The machine can run without the KTI though, you are just unable to use the keypad and touchscreen so for now you may be best off just using a keyboard and mouse until you get the other issues sorted out.

The best way to proceed is to isolate each of the possible causes and determine which is at fault. I'm not sure if you have access to another machine that you can swap components with, but this would probably be the easiest way to do it (as long as the components are compatible).

From my experience, the Realtime timeout alarm is usually an intermittent fault that happens anywhere from once an hour to once a month, but is not a permanent fault as you seem to indicate. In the case of this being an intermittent fault, the power supplies are known to cause this alarm, and is a relatively easy item to replace, so may be a good place for you to start.