I use a CamelBak Cloud Walker (link) which does me well, and I’m carrying a similar amount to you. Laptop goes in a sleeve at the back, clothes go into one of these Eagle Creek ‘cubes’[/url] and then lunch goes at the top. My D-lock goes inside at the back, and cable right at the top.
It would be a push to get shoes in too, but I’ve done it before. I leave mine under my desk, or else have squashable shoes if I must carry them.
The bag doesn’t say it’s waterproof, but I’ve been pleasantly surprised that it has dealt with the worst Scottish weather has thrown at it.
If you’re going on dark roads, you might want to put a reflective cover over it, which would also deal with the waterproofing aspect.