For the xconfmanager part, you can just create a windows/unix script containing the xconfmanager commands.
Seems like it might be a little trickier than that. A windchill shell is built by running Windchill.exe and then passing it a bunch of arguments.
<WT Home>\Windchill\bin\windchill.exe -w "E:\ptc\Windchill_10.2\Windchill" --java="<WT Home>\Java\jre\bin\java.exe" shell
Once that shell is created I'm not sure how the script with my xconfmanager commands would get passed to this new window. Guess I'll have to see if I can replicate whatever that shell setup command is actually doing manually.
Any ideas on the other three areas???