Lightroom is excellent. Couldn't work without it. Are you shooting in RAW
The best way to learn! Straight into M and make some mistakes. Regarding your ISO - personally, I'd always try and keep it at 100 or lower unless you need to move it to compensate for something else.
Ideally, you want to be learning how to balance the aperture and the shutter speed...
I am not shooting in RAW at the moment as I only have a 2GB memory card but as soon as the 32GB card gets here I will be.
I have used the custom settings menu and I have one setup for Night and another for Time-Lapse.
The iso in this camera only goes down to 160, I had a play the other night so I could see how different iso settings worked and what happens if you hold the shutter open for a while and did these:
This is at 200 iso and holding the shutter open for 40 seconds
and these are at 1600 iso:
So that showed me what the iso settings do because to be honest most of this is gobbledygook to me
And this afternoon i had a play with Time-Lapse and did a short video which is poor quality but I just wanted to have a quick play and see how everything worked and here is it: