This just begs the question why dont you simply implement all your stuff in Prototype then - or implement everything in jQuery. Overall they both have the same capabilities.
However to directly answer your question - ther isnt really a way to make a custom build of jQuery. But you could simply put your noConflict
call immediately following your inclusion of the jQuery library.
Then for your stuff you can simply wrap it all in
(function($){
// your jQuery code here... Can be used with $ as normal.
})(jQuery);
within that function youll be able to use $
as the alias - outside of it you would need to use jQuery
. The only gotcha here is that if you want a variable defined inside here to be global youll need to make it that way manually as everything within this will be scoped to the function. You can do this like so:
(function($){
window.myGlobalVar = 'This is a global variable';
})(jQuery);