Whoa there fella. Little too much info, but I'll try to clear up some of your questions.
Power Supply: The opus has connectors that run to the Mobo and HDD's just like any other power supply. The only difference in the way it functions is the input, getting the power from the car battery instead of a wall plug.
Boot times: Everyone is different. But they are not bad. On mine I have music 30 sec. from start coming out of hibernation. A full boot would be longer.
Screens: I can't understand anyone who still buys a Lilliput after researching in the LCD section. But to each his own. If you still want it cause its a good deal just keep in mind that the one you are buying off Ebay almost definately is not under warranty. So when it does fail on you, make sure you donate it to Scouse's backlight project. He needs a couple test screens. Then go buy yourself a Xenarc. Now you've spent close to $700 on screens when you could have done it right in the first place. But don't get me wrong: Scouse really does need a test screen, so get the Lilli.
Where to install: Thats up to you. I am getting rid of my headunit and replacing all speakers. This added a pretty penny to my project. If you do replace the headunit, make sure you find the right amp for your speakers. From what I understand most stock speakers are 2 ohm and would sound like crap amplified.
Good luck with your project.