While I just add my most used apps to the dock, and have my Applications folder added so I can access everything else like this, I've just coded up a (very) quick AppleScript folder action that probably does what you're wanting.
Here is the .zip file with the script. You'll have to do a couple of things to use it though.
First, enable folder actions by right-clicking anywhere in Finder and choosing the Enable Folder Actions option. (I've found it sometimes needs you to log out/in before it takes effect)
Unzip the file, and put the .scpt into:
"macintosh hd: library: scripts: folder action scripts"
I've found that for some reason, action scripts don't seem to run unless they're actually in this folder. (or an alias to them is) Strange that it lets you choose the file from anywhere, but only seems to work when it's there.
Now that you have the script file in the right place, we need to decide where we want our "start menu" items to be stored. Just for testing purposes I created an "aliases" folder in my home directory, and added that to my dock.
Create a new folder wherever you want to store these files, add it to your dock and then edit the .scpt file and add the path to it.
The path I have in mine is "Powerbook G4:Users:andrewfee:aliases"
Powerbook G4 is the name of my hard drive (defaults to Macintosh HD)
and the Users:andrewfee: is the path to my home directory
aliases is the folder I created there to store these files, but you can put it wherever you want, as long as you put in the correct path.
Save the file, and then go to your Applications folder. Right click here, and attach the folder action to your folder. Now whenever any file is moved into the applications folder, it will be added to your custom menu. You can just left-click on this to open it up and remove any unwanted ones, or customize it as you see fit.
Like I said, this was a very quick job, so it will add an alias to
any file dropped into the Applications folder (although that
should only be apps.
) I'm quite sure it could be improved upon, but it should do the job.
I hope this helps.
I can't really help with the second issue though, as I've never had a problem with the way this has been done.
Now, it won't create aliases to items already in the applications folder, but you can easily add them yourself, and whenever anything new is added, it's done automatically.