I have the Opus 150W PSU and it powers the CPU up after I turn the key, as far as I know this is the way it operates and. Aside from adding a switch ourside the PSU, there is no way to change this. As for power down, there is a jumper on the PSU (you need to open it up) and it has 3 settings (I think they are 30sec, 20m or 40m) which determines the time after the key is removed that the PSU will shut the system down. This should all be in the manual.
As for the Lilliput powering on, it does not power on by default when it gets juice normally (though I have read that some newer ones will do that, but does not seem to be the case for mine). In order to get the Lilliput to auto power on when power is applied you will need to break out the soldering iron. There is a mod in this forum, just do a search for Lilliput auto power" or something like that.
Regarding how long to boot, that is dependent on your setup and too many other things to list - you just need to tweak it. There have been threads here showing how to disable services (also check www.blackviper.com) - you can also go as far as changing the shell to speed up the boot time.
Wear and tear wise, I am not sure, but I doubt it will have a great effect considering the other wear and tear issues with a carputer (heat, vibration, humidity).
Good luck, looks like you have the start of a nice system.