You will have problems with this, no matter how you go about it. Each step is a little more unusual it seems.
You'll need to use a source code obfuscator to protect your source. I recommend the one by Zend, not from experience, but because Zend makes awesome products. Never used a source protector myself.
You'll need three custom LAMP/MAMP/XAMP installs, one for each target OS. They should point to a directory that is shared on the USB drive. Make sure you configure them to use an unprotected port, otherwise the user will need admin privileges to run the server software. And getting the server stuff up and running will likely result in a few hiccups as well.
I would actually recommend finding something that will allow you to distribute a binary, or something like an AIR app that is intended for this type of distribution. You may have to rewrite lots of code, but it'll be easier to fix than all the niggling little install errors you'll see on the client end. To package scripts into binaries without rewriting stuff, check out http://www.scriptol.com/apollo.php and similar products.
But I'd suggest you make a standalone app in adobe air that will sync with your server (maybe even some google gears integration, to have it function offline). Don't try to force a PHP app into this distribution model, it'll create nightmarish problems.