I beleive this is your first thinkpad
1. The green light near the side of the machine is for your optical drive. I hope you know that it is hot swappable (meaning you can remove it when the computer is switched on) and the green light shows that it is inserted into tha machine. The optical drive sits in a bay called the 'Ultraslim bay' and is removable. You can replace it with a secondary battery or a 2nd HDD adapter with an additional HDD for extra storage.
2. As regarding the sleep function of the laptop on closing the lid, I dont know of any way to change this behavior automatically between docked and undocked cases. I beleive that you can leave it in sleep mode permanently after you set up the proper docking setup you want as regarding to the screen resolution. I use a mini-dock at my workplace often and I have had no trouble docing and undocking it.
3. Try using the Fn+F9 combination to launch the easyeject utility for removing your USB harddrive if the default windows one doesnt work properly. Choose "USB storage" in the program and run easyeject actions. This has always worked for me.
4. I don't know about time settings in windows vista since I run XP pro ... maybe someone else can help you there.
5. I don't use the IBM message center at all. I disable it from running and use the Thinkvantage System Update periodically to see if any updates are available. (This is found under Start-->Thinkvantage). System Update is a fantastic tool to keep your laptop upto date and I suggest you reply on it than IBM message center.
6. Don't be bothered about the indicator light, sometimes that happens.
7. Regarding seting up a new profile in the presentation director, do the following steps: (dont dock the machine while doing this)
a. Press Fn+F7 to launch the presentation manager, Choose more schemes and press 'New' in the next dialogue.
b. Press next on the first screen, and on the 2nd screen choose your monitor type (Analog/Digital). Uncheck the Thinkpad LCD option in the top of the screen and press next.
c. Choose the resolution you want in this screen, and press test to check the display (you have to have your monitor connected to the laptop for this ... if you are using a monitor with a DVI input, ignore this step). You will see a screen on your external display and your thinkpad display will go blank. Press close on the external monitor
using your laptop mouse and you will get back the display on your laptop.
d. Ignore all options in next two screens (press next on both without checking any options)
e. Give a name for your setup and press OK.
f. You will come back to the presentation director. Now check the 'Immediately apply this scheme' when thinkpad is docked and choose the shceme you just created.
g. you dont' have to bother with sleep settings on your laptop, but I strongly suggest you keep it under sleep mode while the lid is closed.
h. Close your laptop and your machine will go to sleep. Power your dock, connect the monitor to the docking station. Dock your laptop and press the power button on the dock - if all went well, the external monitor sshould work fine now. If there is no dispaly or anything, simply undock the machine by pressing the 2nd button on the docking station, wait till it turns green and then unlock and remove your machine and check all steps again.
If this does not work, let me kno what problem you are having and I'll try to see what went wrong.