Don't worry, you'll get it back together. You've only got one set of parts and they all have a home. If you end up with 'extra' parts when you're done, just start over!

Seriously, you'll be fine. You definately want to replace the cables and housing so just cut the cables off if they get in your way. I'd keep the old housing around so you can match the lengths but do replace it.

Elbow grease and a rag is usually enough to clean most parts. You can always use plastic bristle brushes without worry but I'd avoid scour pads and wire brushes.

I'd also recommend keeping all the parts together, zip lock bags work well for this. Ie, if you disassemble the brake calipers for instance, put all the screws, springs, arms, etc from the front caliper in one bag, all the parts from the rear in another bag. Ditto for any other parts. That way you won't get the various tiny parts mixed up.